Definitely agree with Stadler. I won't go into specifics to avoid unnecessary diversions into P/R territory, but, as an atheist, there are plenty of political proposals that I find as entirely unsubstantiated as belief in God. And many of those proposals are expressed in far more personally offensive terms than Neal's lyrics about Christianity. It might be a different situation for me if Neal was constantly singing about how those who don't believe in God are worthless people who deserve nothing but scorn. But that's not what's going on.
And just from his music and onstage persona, I get the sense that if I met Neal, he would treat me with complete respect and kindness even if he knew that I am not religious. People here who have met him can correct me if I'm mistaken, but even if he's secretly a jerk in person, that's certainly not what he puts out in his music and persona. Whereas I have no sense at all that, to go to the extreme opposite case, Roger Waters would show any sort of respect to someone who disagrees with him about Israel.