Does religion always equal good?

It’s a compelling question.  In response to criticisms that the intent of the book, The Golden Compass (soon to be aired on the big screen), was to promote atheism or anti-Catholicism, author Philip Pullman had this to say:

In the world of the story — Lyra’s world — there is a church that has acquired great political power, rather in the way that some religions in our world have done at various times, and still do (think of the Taliban in Afghanistan). My point is that religion is at its best — it does most good — when it is farthest away from political power, and that when it gets hold of the power to (for example) send armies to war or to condemn people to death, or to rule every aspect of our lives, it rapidly goes bad. Sometimes people think that if something is done in the name of faith or religion, it must be good. Unfortunately, that isn’t true; some things done in the name of religion are very bad. That was what I was trying to describe in my story.

I think the qualities that the books celebrate are those such as kindness, love, courage and courtesy too. And intellectual curiosity. All these good things. And the qualities that the books attack are cold-heartedness, tyranny, close-mindedness, cruelty, the things that we all agree are bad things.

You can read more about what Pullman had to say here.

What do you think?  Is it fair to criticize religion?  Is that the same as criticizing God (however you interpret God)?