The conservative talking point against gay marriage is that it will somehow undermine "traditional" marriage and the culture at large. It comes from a standpoint of quite literally being afraid of homosexuals and homosexuality.
I think it's fair to assume that Brenden Eich's reasoning shares some of those features. (Or he donated that money cynically for some other reason. I suppose that's a option.)
Either way: He gave money to prevent an entire class of Californians from enjoying their rights. Which is a pretty shitty thing to do.