I suspect a lot of the ones voting yes do it for other reasons than themselves being offended... atleast by the notion of religions having special abilities.
Crusades, Suicidebombers, Pope, Reformation, Jihads, DalaiLama, Ayatollahs etc...Most of us do some sort of association to religions when we hear these things. I agree that the examples given in the first post could have been better chosen, although suicidebombers have a pretty strong link to Islam in people's minds, and that's what matters.
Even though I think it's pretty boring the way Firaxis seem to be implementing religion in the game, I suspect it's to keep it easily balanced and with enough freedom for the player. More of a new diplomatic/cultural layer than a true religious historical path which might be harder to accomplish in a good way and probably not exactly what the civfranchise is about. Too bad - the Pope is threatening me with excommunication again in M:TW, annoying, but still very fun.
edit: typo