The purpose of organized religion is to make money. Just like a corporation. If you are not a customer who is buying their product, you are not making organized religion money, and you are therefore a problem.

People fear what they don't understand.

I think a lot of it has to do with them not understanding what an atheist really is.

How many religious people would give the wrong definition when asked, I think the majority would call us devil worshipers.

Seems to me outgroup tolerance is about equal on both sides.

They are indoctrinated not to listen to others belief systems.

probably because part of their doctrine implies superiority or demands conversion. Why is a hard question to answer

One of the basic tenets of most religions is that it is the only allowable belief, it is right and everything else is wrong, usually evil and must be eradicated.

Militant followers are in both. We need to consider the other person as fellow human despite his/her/other inconsistencies and beliefs. Just like what @AccursedHalo said, there is a threshold for every person beyond that the person may become intolerant of others view. That threshold is person specific. In some cases, the mob behaviour also take precedence over our personal feelings. That's what I feel.

I think every one is tolerant to a certain point. What that point is? Depends on the person. Some days I just CAN NOT deal with religious people and I hope they all die. My ex-friend Erica was tolerant of me and my against religion memes. But one day she finally snapped because a meme or something I shared involved Catholics. She was not happy and she unfriended me. :/

Believers do not think atheists are tolerant of them. They have convinced themselves that we are "at war with Christianity", assaulting Christmas, etc. They see us as the aggressors when we do not want such things as "...under God..." in the pledge and prayer in school.

Because their interpretation of their Holy Book states they have to save us from Hell. They feel they have failed if they don't.

Probably because they are the majority. Power corrupts.

Because their religious beliefs form the core of how they define themselves. Without that, they are lost and that thought threatens them hugely.

I know tolerant Christians.

Simple. All Abrahamic religions require their believers to proselytise.

Because they need to save everyone from eternal hellfire, or else. It's literally encoded into some religions. Also, why are we pretending here? lol

Cognitive dissonance

We know and are willing to accept our fate. They do not know (despite their assurances to the contrary) and they do not want to have anyone be the cause them questioning their own. cognitive dissonance is a powerful force for everyone (question a liberal about some things they take seriously - like immigration, charity or giving food).

When my partner was dying I personally experienced the anxiety of death. Even though I would have been more than willing to trade places it was still unnerving.
@VictoriaNotes

Also, they don't like to have logic interjected into their dogma. It undermines all of their fantasies.

Tolerance is not in the characteristics of religion.

First, what does an atheist represent to the believer? If we appear to be happy, well adjusted, moderately successful, well educated, and doing good in our community we stand as a glaring contradiction to everything they've been told about us. That's just for starters. We also are a reminder of their insecurities. These folks have to keep reminding themselves of what they believe and make sure it's all held firmly in place, then along comes someone who seems to be secure and content without all those things they're supposed to remember. Then there's the ultimate worry. They can't face the idea of it all coming to an end. Surely there must be something better on the ... other side, right? Standing there as if nothing at all is wrong is someone who doesn't have all that worry.

It is just a matter of time, usually not much time, before they are moved to explain to that person that they need to be saved. That they need to be worried about heaven and hell and the eternity they will face in the Lake of Fire if they don't repent from their ... uh ... from their what? ... wicked ways? Damn, the only thing that atheist is doing wicked is ... is ... not believing. How can anyone not believe? This is not possible. Everybody believes in something, right? That's what they're doing that's wicked. They're believing in something wicked. Like what? Melt down will surely follow if something is not done.

They can't tolerate us. Not only because of what I've said here, but because their deity, the one they believe in has said that we are not to be allowed to live. That we are worthy of being drowned in a great flood or stoned at the city gate. Fortunately, there are some who do not buy into all that crap and have figured out a way to tolerate us and the LGBT community -- at least on the surface. I suspect that down deep in the mental cellar they are quietly stoning us too.

Do not expect genuine tolerance or understanding because it cannot be given. We can and should give it to them, but they can't reciprocate 100%.

Same reason alcoholics prefer to be around drinkers?
I'm tolerant of religion until it butts into my bank account, my kid's education, my right to share this planet without fear, my home and my space to think freely without being told my feelings/beliefs are wrong. Unfortunately, religion has in some ways, done all of that. So I'm kinda pissed and kinda thinking appeasement may not be the way to go with this.