This article from Slate is really long and really good and basically summarizes how Tom Cruise is not the first or second or even fifth choice for film projects anymore and how Katie severely damaged her career with her actions during promotional appearances for Batman Begins. The article briefly mentions Scientology, but it is not a focus of the article. Like I said, the article is long but it will give you something to read over the weekend. If you are really bored this afternoon you can watch the two segments from David Letterman that allegedly caused Katie's career spiral.
Thanks to Mistik for finding the article and sending it my way.