Dunno--maybe he thought he could better serve Alaska outside government than inside...
If I had to guess, I'd say it was a combination of two things: The looming New York pension fund investigation, and the fact that the dealmaking portion of the auto bailout is basically over (and pretty successful). By which I mean, I'm not sure there was anything in the investigation that was necessarily going to force Rattner out in itself. (The inquiry is into whether Rattner's old employer, The Quadrangle Group, paid a middleman to become one of the pension fund's money managers.) According to the Times story, the potential charges here are civil and Andrew Cuomo basically wants Quadrangle to pay a big fine.
On the other hand, everything we know about Rattner suggests he had ambitions that went well beyond the auto bailout. As the Journal's piece put it:
When he jumped at the opportunity to spearhead the Obama auto task force, many in Washington assumed he would later ascend to other jobs at the Treasury or the White House.
And obviously that wasn't going to happen once the pension investigation came to light. Given that, Treasury's explanation for the timing of the departure makes a lot of sense to me. As Tim Geithner said in a statement quoted by the Journal:
Mr. Bloom [Rattner's successor], he said, would lead the effort now that it was moving away from "day-to-day restructuring to monitoring this vital industry and protecting the substantial investment the American taxpayers have made" in the companies.
That doesn't sound like a job you particularly need Rattner for--nor one that would necessarily excite him.
P.S. Of course, you can't underestimate the "Chooch" factor. Per the Times:
Investigators have been particularly focused on investment executives who arranged for payments to be made to further the production of “Chooch,” a low-budget movie produced by the brother of David J. Loglisci, who was the chief investment officer of the New York State pension fund under Alan G. Hevesi, the former state comptroller.
Investigators believe a number of executives, including Mr. Rattner, gave assistance to “Chooch” to win pension fund business.