No one (that I've seen, anyway) is ragging on Brendan Eich for being a Christian. I don't even know whether he is, although it's a fair guess given his decision to support Proposition 8.
Many people are saying that Eich's support of Proposition 8 is a bad thing, makes him a bad choice for CEO of Mozilla, discourages them from using Mozilla's products, etc.
Attacking someone for being a Christian: religious bigotry based on disapproving of someone simply on the basis of their identity. Generally a bad thing.
Attacking someone for supporting Proposition 8: disapproval based on what the person has actually done and its likely consequences. No reason why it shouldn't be a reasonable thing.
This doesn't seem to me to be a very subtle distinction.
(Aside: I do find it curious that of the four people who first come to mind when I think of Mozilla -- Mitchell Baker, Gervaise Markham, Robert O'Callahan, Brendan Eich -- two are rather vocally Christian (gerv's blog is called "Hacking for Christ"!) and a third has become infamous for an action that's probably the result of a similar religious position. Just coincidence?)