Tolerance?

I pride myself on being tolerant. I'm always getting into discussions about topics such as separation of church and state as well as homosexual marriage (also known as marriage equality), and one thing I am constantly telling the opposition is that not am I only supporting human rights in these cases but also of general tolerance.
I am of the opinion that if people just bit their tongue in many cases, then this world would be a lot better off. Much easier said than done, I know! I've come to realize that some people are just not going to change their opinion, and some just don't want to.
Now this is not to say I expect  everyone to have the same opinion as mine or change their way of thinking to suit me, not at all, but when the behaviors, actions, and opinions of a person fall into the categories of racism, homophobia, hatred, etc., then I draw the line there.

This is 2009. Not 1909. Cliche, perhaps, but time does stand as a testament to historical behavior. We, as mankind, have progressed much further than those living 100 years ago could have possibly ever imagined. There is really no excuse for human rights violations and derogatory words/behavior nowadays.

Here's my confession, though: I find it becoming increasingly more difficult to "practice what I preach" when talking to the majority of Christians. Don't get me wrong, persecution whether physical or verbal is always wrong, so my tolerance will always be. While I do this, it's still difficult not to just exclaim, "How can you be a smart person yet so delusional when it comes to religion?!"
I have religious friends on Facebook, MySpace, etc., who are so unbelievably open-minded that it almost shocks me. These friends also believe in marriage equality and would love nothing more than to have their children's education stay in school and worship only at home/church. I love that they defy the stereotype of what a Christian is often known to be. At the same time, though, I see that and think, "You're only one step away from non-theism, what is holding you back?"
I know they're not the type to rely on their religion to get through the day, because I've witnessed first-hand those who do. I am failing to understand what it is in religion that they feel is accurate or truthful. This is my natural bias, as an Atheist, and I fully understand that some will not be able to comprehend how I don't believe in any deities.

So perhaps it's not tolerance which I am lacking, rather it's the inability to grasp how a person can be so rational and smart in other areas yet still believe in an invisible being with supernatural powers.