An Honest Question

Let me start off by telling you about what I did this evening, because this question requires a bit of back story. I went to my parents to visit while my sisters Kristy and Kelly were there this weekend.
My sister Kristy and I went outside to look at my paint job on my car, since she didn't get to see the finished result when it was being painted (by her husbands body shop) since they left for vacation at the time. Upon seeing my Obama bumper sticker, she told me:

"I cant believe you have that man's bumper sticker on your car. I ought to rip that off."

Okay, now I was intrigued. I asked why she felt that way, and the answer floored me.
Apparently, her church regularly preaches to them that Obama is a Muslim terrorist, and the Antichrist. He's plotting to destroy America from the inside, planted by the Muslim extremists.
Yes, you heard me right. This is being preached by a church.

This raises a couple questions for me.
Number one, why on earth is this church taking it upon themselves to be spreading this kind of misinformation and slander?
The real question I want to ask I'll get to in a moment.
Needless to say, I tried my damnedest to convince her that the church was spreading propaganda, but I don't know how much damage I was able to undo.
Through this conversation, we eventually landed on my argument that even if Obama were a Muslim, what difference would that make. I made the point that America is made up of Christians, Jews, Muslims, atheists, agnostics and a whole colorful rainbow of creeds. What would be the problem with a little Muslim boy or girl who lives in the Unitest States wishing to grow up to be President someday?
The answer I got really made something in my head kind of click, and I can't really explain how it made me feel.

Because they would believe in a different god than her god, and that would be wrong.

Myself not being a person of religion, I don't know the answer to this, and I know most anyone who is reading this who knows me is not a person of any strong religious ties either, so I ask this in the hope that maybe some anonymous reader who is could answer it for me.

Does being loyal to a certain religion in this day and age make you intolerant of other religions?

I really want to know. Myself being agnostic I understand that there are many deities worshiped by many different groups, and thats okay. What I really do want to understand though is if being religious and dedicated to one group makes you see others as 'wrong', or if this is simply another product of the apparent radical approach that my sisters church takes in 'teaching' their congregation?