I value religious believers and nonbelievers alike. I recognize that religious belief (or non-belief) does not make someone a good or bad person by itself. I support religious freedom, and I believe that one should have the right to practice one's religion in the privacy of one's home or place of worship as long as one does so in accordance with the law and does not inflict harm on others. I also recognize that true freedom of religion is not possible unless it is accompanied by freedom from religion. At the same time, I would welcome a gradual erosion of religion's political influence to the point where it was considered a private matter that did not intrude into the public sphere. Does this make me intolerant?
As long as nobody is harmed and no valid laws are broken, people should be free to practice their religion (or lack thereof). Religious belief is supposed to be between the believer and his or her god(s). There should be no state interference in such matters, be they positive or negative. The believer deserves this freedom every bit as much as the non-believer does.
In fact, I'd like not to have to care what a believer believes. I'd like to leave that completely up to them and not concern myself with it. If religion could somehow be divorced from politics and if I could escape the constant bombardment by Jesus music when I'm shopping or door-to-door evangelizing when I'm at home, I could probably remain content to remain oblivious to what religious folk believe. Maybe I'd examine it as a curiosity, but it wouldn't have great relevance.
But many believers insist that part of their religion involves frequent attempts to poison others with it. It is not enough to believe; one must actively try to spread one's belief. They do not appear willing to give this up. Moreover, believers are not content to forgo their forays into politics. Evidently, their religion is less meaningful if they cannot impose it on others and restrict their freedoms.
Given the massive influence religion has on politics and the degree to which it repeatedly leads politicians to make horribly destructive decisions (e.g., denying global warming, preventing stem cell research, launching preemptive wars to fulfill end-times prophecy, etc.), I simply do not have the luxury of ignoring it. Given the frequent intrusions by believers into my personal domain, I have little opportunity to ignore it. Instead, I must work to defend reason and oppose religious extremism.
Does it make me intolerant to wish that religion was a private matter or to long for an end to proselytizing? Does it make me intolerant to dream of a reality-based politics where decisions were made on the basis of sound reason, evidence, and science? Does it make me intolerant to wish I could get through two consecutive days without hearing about Jesus?