I'm a very active Catholic, and I can't say I have any problem with any of the songs listed. "Stand Up for Judas" gives me something to think about, and I don't find it offensive. I learned "Plastic Jesus" and "Vatican Rag" and Has Anybody Seen J.C. at a Catholic seminary when I was a student there in the 1960's - I suspect all three of these songs were written by Christians of the liberal persuasion, which is where I fit in the spectrum.
If it were a song that expressed hatred for believers, that might be something I'd find offensive. I think most atheists just don't believe in God - they're usually a lot more tolerant of believers, than believers are of them.

I gotta say there's one "atheist" think that has found popularity that bugs me - it's that walking fish with the word "Darwin" in it. It's a parody of the popular Christian fish symbol. I suppose it's kind of funny, but it give the incorrect implication that Christians don't believe in evolution. It's true that some Christians don't believe in evolution, but most Christians I know believe that God created and is still creating the world through the wonderful processes of nature, including the process of evolution.

-Joe Offer-