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When some humans, humanoids and mythical creatures have an incredibly powerful magical regeneration it seems quite obvious that in times of need and growth some countries would try to capture them and use them as ''basic resources''.

This is not really a spoiler because it's on the first 2 pages of the book but
one example is Fire Punch, in order to survive a kid is using his magical regeneration to create food and burning fuel by chopping his limbs continuously.

One real world example is Culling, basically creatures bred and tortured for the only purpose of creating easily accessible resources, whether such creature dies or lives is based on their ability to produce such resources and being spared and surviving might actually be considered a destiny worse than death.

I believe it is historically accurate to assume many kings, queens and people of power would have indeed enslaved such ''people'' and used them for things likes experimentation, food or flesh-shields ... or for pretty much anything actually ...

There are different means of getting the magical automatic regenerative abilities, some of them are either training to become a magical healer or simply being born in a magical forest or being born from parents who had this ability, so it is quite common and they are spread across a world with many far apart isles, almost like if our world had been broken into small pieces distanced by water. Technology is mostly pre-victorian and a few empires and nation have powerful artifacts created with a mixture of engineering and magic, those artifacts can be used to create portals, transform lead into gold and other things...but they are incredibly rare. The rest of the world is made by mostly tribes and villages.

What is the best way to protect self-healing creatures from being turned into slaves?

Religion is excluded because in my setting deities do actually exist but everyone knows they have no say on the subject. A powerful cleric could simply ask a god or goddess if she or he have anything against it and they would respond that they don't care.

Yes, the energy and materials needed for regeneration are infinite and come from magic.

If they can choose whether to use their powers or not, they could simply refuse to regenerate when being enslaved and die instead.
Edit: As you changed your question to what you could do if it was an automatic process.

You could have the cut off limbs magically disappear so they couldn't be harvested.

It's also historically accurate to suggest the principles of serfdom meant that most of the population were barely better than slaves anyway. Even direct slavery itself was normal until relatively recently and still goes on in many places.

The modern concept that people should have freedom really is a very modern concept and any historical setting should include a fairly solid level of slavery and indentured servitude.

For your character to not be a slave you'd effectively need them to be a member of the nobility.

This depends a lot on whether the rulers of this world act like real world medieval nobles did. If the gentry behave like history would suggest, they'd want to turn your regenerating creatures into literal meat for the machine and little short of the ability to resist their will would dissuade them. As such, your self-healing folk have but two realistic courses of action: exodus or rebellion

Of the two, exodus in the form of self-imposed exile would happen spontaneously all the time since that's just a matter of individuals choosing to hide where they think/hope they won't be persecuted. However, it's untenable in the long term unless they can find somewhere uninhabited by regular humans to settle in. Attempting to hide in lands ruled by the gentry makes it only a matter of time before discovery and capture.

Which brings me to the bloodier option: a rebellion of regenerating folk banding together to fight for their rights. This could easily become a popular uprising if they tap on the grievances of regular human peasants to convince them to join the cause. A clean victory for the rebels would most likely lead to a new nation being carved out, where the regenerating folk rule over their own kind. Otherwise semi-autonomy or power-sharing could be arranged, but these are definitely the less appealing options that would happen only with a win through compromise. In the long run, it's unlikely the regular human nobles will honour such a deal.

Perfect regenerators are much more useful as a warrior caste than as a slave caste

Nobles want to win. In pre-victorian era, that's tied pretty directly to the ability of your armies to win on the battlefield, and in one-on-one fights, and regenerators have a huge advantage there. If you have only a small percentage of your populace as regenerators, you're a lot better off training them as warriors and ensuring their loyalty than trying to turn them into some sort of horrific food source. The real trick is going to be preventing them from taking over the nobility entirely (as entrance into the nobility was also generally based on prowess in battle)

Admittedly, there might be kingdoms where they turn their regenerators into food sources... but the kingdoms where the regenerators are warriors should be able to pretty trivially overwhelm them using regenerator armies, free the food-source regenerators, and thus add to the size of their armies while improving morale. (Things like "desperate gratitude" and "freeing kin kept in horrific bondage" will do that for you.)

There isn't much historical precedent to suggest that [intelligent, humanoid] creatures would be used as anything "worse" than a slave. Regenerative abilities don't change this.

I'm normally pretty cynical, but there were not a lot of cultures which regularly engaged in cannibalism - even of foreigners. This was true even of when it was an explicitly held belief that the natives were natively / culturally superior. I doubt it would make a difference that the foreigners would have their limbs grow back.

It isn't just the impracticality of cannibalism that makes it rare in a stable and cultured society. "Civilization" itself would prevent such a gross abuse. There have been terrible atrocities throughout history. Human beings are capable of incredible brutality against "people." But we notice the furthest extremes of that brutality precisely because it is exceptional. Dehumanizing others, working them to death, starving them? Historically not rare. Eating them? Only when society is objectively broken, even by standards much lower than are currently held.

Magic escape hatch!

Your "energy and materials needed for regeneration is infinite and comes from magic." So regenerators are tapped into a source of magic for their powers. If you want them to be unenslavable, have their power come with an escape hatch - they can physically go to the source when they choose, disappearing from their environs and appearing at some designated place corresponding with the source of their power. This could be some temple, or ancient cave; you mentioned enchanted forests so some power grove in the forest.

The retreat place might not be the same place for each individual with powers, but probably one source / place would supply multiple individuals. There might be reasons an individual would not want to go there - like it is a long walk back home from there, or they will have to serve the powers there for a time, or they will have to wear a silly hat and eat a bug. Maybe escaping thus is a one time thing and by making that escape they lose their regeneration powers permanently. Or maybe it is into the black - once they go they cant come back; a voluntary death equivalent for individuals that otherwise by virtue of their powers elude death. Whatever you want to dream up that will make this escape method something they don't do all the time but can do in a bad situation.

Regenerators could still be made to serve, and might still be slaves, but the people imposing conditions on them would have to be careful not to push an individual too hard, or that individual will disappear and be lost to them.

Consuming pieces of the regenerators is known to cause undesirable side effects such as uncontrolled growth or mutation of ones own cells otherwise known as mancer the magical form of cancer.