'Religion' is a hierarchy of values that someone chooses to observe, respect, and follow. it guides thought, action, and belief, for better or worse.

I can run into a religion that I find distasteful. This is possible. Perhaps it calls homosexuality a perversion, or condones a caste system. These are things that I disagree with, ideas that my value structure cannot line up with.
I still take each member of that religion on a case by case basis, because I've lived long enough to know that people are hardly ever defined by the religion they subscribe to, and I've found plenty of good, caring, reasonable individuals who happen to be Catholic or Baptist or Jewish. But I can still say that the religion itself is horribly twisted in many aspects. And when I'm in a room with a Catholic, it makes sense for me to be a little more cynical than otherwise. I know that this person probably has many beliefs that are in stark conflict with mine. I'll give them a fighting chance, but I won't be terribly surprised if they don't surprise me.

This is entirely different from racial hatred.

Racial hatred is based in xenophobia, the fear (and, in three easy steps, hatred) of anything that is different. 'Dark skin? That's different! I don't know what to make of that; I'm afraid of it. I hate things that make me afraid!' It's never quite that cut-and-dry, but it almost always follows that template. You have no idea what philosophies or ideas that person might subscribe to, none whatsoever. And yet you judge them. On the tone of their skin, or the shape of their face, or the size of their nose. It's all the same.

I judge people by the quality of their character, the actions they choose to take, and the ideas and beliefs and morals they subscribe to. Religion is part of this. This is how I judge people, and I find no shame in it.

Other people judge people by the firmness of their handshake. I think that's just silly.

And others judge people by the shade of their skin, or their accent. I think that's just as silly, but it usually takes a much more horrid form.

Hating religion is different from hating an ethnic group. One makes sense. The other does not. Some may say it is more complex than that. Well, I think that sometimes it is just that simple.

I think it's more than a little depressing that this idea can even be argued.