Nominally, he's stepping down to spend more time with his family. The blogosphere, of course, is wildly speculating on the "real" reason he's quitting at this point in the Bush Presidency, and of course your wild-ass speculation is as good as mine.
Just to throw out some paranoia, though, I'll opine that Rove is getting out of town now before Congress realizes that (a) the District of Columbia government works for them (see Article I, section 9 of the United States Constitution), (b) said District of Columbia has police, prosecutors, etc. who don't report to George Bush, and (c) no Federal law enforcement personnel reporting to said George Bush will arrest people (like, say, Karl Rove) who blow off Congressional subpoenas due to claims of executive privilege by said George Bush.