My facebook feed in the last few days is full of "why only Hindu bashing in this movie PK" statuses written by highly offended Hindus and duly shared by moderately offended concurring friends. I thought I'd add my contribution to all your feeds too in response because i'm tired of being the mute receiver of such distressed cries.
First of all, the movie does not shun Hinduism or faith in general. At the risk of giving out spoilers (I know! hah!) they clearly show how equally ineffective every faith's method of prayer is. They were unable to touch upon Zoroastrianism, Judaism, Buddhism (?), Confucianism and Scientology. Maybe the movie makers don't like them either (or maybe they consider these ones perfect).
More importantly, they have been careful enough to not go down the atheism angle. Said Gods might know what would have happened had they done that. Or maybe that would have been a good thing. The Hindus would not feel all singled out then. The movie embraces faith but with sane viewpoints that one would expect most educated theists to already be in possession of, or at the very least not be offended by. (Oh List it out you say?) Use common sense, don't be swayed by the myriad 'godmen' in existence, take care of ailing family before leaving on a pilgrimage to heal them, don't expect a prayer/10 prayers/100 somersaults to change your life and so on.
Having said this, the movie is not all that great. It has many genuinely strong laugh-out-loud moments, good dialogues, but the songs are unnecessary and a complete drag, multiple scenes are redundant and a few scenes to the end are so ridiculously cliched we managed to squeeze a few good laughs out of those as well.