She was a proto-humanist in more ways than one. For example, she said, “Reserve your right to think, for even to think wrongly is better than not to think at all” and also that “fables should be taught as fables, myths as myths, and miracles as poetic fantasies. To teach superstitions as truths is a most terrible thing.”
We’ll never know conclusively why Hypatia was murdered. However, we do know that she said this:

In fact human beings will fight for a superstition quite as quickly as for a living truth—often more so, since a superstition is so intangible you cannot get at it to refute it, but truth is a point of view, and so is changeable.

Yes, that’s a humanist point of view!