If you make comments that are critical of someone's religion or politics or social beliefs or whatever, some number of people will find it annoying or offensive and be uninterested in reading your stories.
Take the flip side. You say you're an atheist. Suppose you read a book that had many sections that attacked atheism in one way or another. I'd guess that as you were reading you'd be thinking of rebuttals to these attacks. But at some point wouldn't you be likely to say, "I'm tired of reading all these attacks on my beliefs and opinions. I just want to read a fun escapist story, not a religious or political diatribe!"
Let's face it, you don't have to be a closed-minded bigot to say that you just don't want to get into a debate right now, you want to relax. If I was running for office and in a formal debate my opponent challenged some political belief I had, of course it would be absurd to say, "How dare you criticize me! I refuse to discuss this. These are my beliefs, and you should respect them!" But if I'm sitting at home, tired after a hard day of work, and I just want to read a light novel and relax, I might well not want to get into a debate. I just want to read something fun.
All of this would, I think, depend a lot on the nature of the comments and the attitude of the reader. If the comments are rare and mildly worded, a reader might just brush them off and get on with the story. If the comments are expressed in serious philosophical terms and not just nasty ridicule, a reader might find them thoughtful rather than offensive.
I'd especially say that if your comments are vicious attacks on caricatures of someone else's beliefs, I mean if you make statements that make it clear that you have no idea what your opponents really say, but you are just taking any negative statement about them that you can think of, distorting their views to make them sound as absurd as possible, etc, then people are going to be much less interested in continuing to read your work.
I'm a Fundamentalist Christian. I've read lots of stories by atheists that criticize Christianity. In a few cases, the criticism has been intellectually interesting. Like a writer might bring up a point of Christian belief or practice that is not well thought out or consistent. In some cases I'll say, "Hmm, that's a good point. How can I respond to that," and it leads me to think. I'm hard pressed to think of a fiction story that has led me to seriously question my beliefs, but some have been interesting.
But frankly, most atheist attacks that I read on Christianity are just silly and annoying. The writer clearly has no idea what Christians really believe and he's just hurling insults. I'm not going to knowingly buy a book whose purpose is to make rude, gratuitous insults against me. This is not a comment about atheism, by the way, but about specific writers. I don't doubt that there are Christian books that make childish insults against atheists, or Muslim books that make childish insults against Hindus, etc etc.
And just by the way, as a Fundamentalist Christian, I don't find anything about the paragraphs you quoted in your post insulting or offensive.
Oh, and one more by-the-way: If your PURPOSE is to challenge people's religion and persuade them to change their beliefs, then of course the idea that this might cost you some readers is just a price you have to pay. Then the issue becomes, What is the most effective way to get this material into my story? If I'm very blatant, will I shock people into realizing the absurdity of their beliefs? Or will they tune me out before listening to what I have to say? If I am very subtle, will people skim over it and miss the point? Or will I slip thoughts into their head that might germinate later? Etc.