Watterson explicitly stated that the names have no relation to the characters' personalities or philosophical views. As someone familiar with John Calvin's views and writings, I can say safely that Calvin is not much in any way similar in personality or spirit to anything John Calvin ever taught or expressed. At best, Watterson is projecting the typical libertine caricature of John Calvin as a cantankerous and disagreeable curmudgeon onto the character. John Calvin was in reality quite progressive for his time, and by all impressions did all that he did out of love for those around them in line with a plain reading of scripture. But to see him that way requires nuance that seems to be lost on the anti-religious.

The joke is that Calvin is aligned with Hobbes’s philosophy and vice versa.

No? Like d-us-vb said, the characters' names have nothing to do with their personalities.

Yes, they occasionally discuss philosophy.

No, that does not mean that the philosophy being discussed has any relation to John Calvin or Thomas Hobbes.

The joke is that they're a kid and a stuffed tiger named after philosophers.

Disagreeing with the idea that your fate has already been sealed no matter what, and that you have no real agency in the end has nothing to do with being anti-religious. Furthermore, I am not anti-religious