Why Thomas Won't Be The Next Chief Justice: Edward Lazarus offers his take at findlaw.com. The core of the argument:

  Bush will . . . pass over Thomas. Why? Because, I believe, he and his advisors will ultimately decide that, ironically, appointing Thomas to be the next Chief Justice would probably disserve their goal of advancing a more conservative agenda at the Court.
  . . .
  The most influential Chief Justices - the John Marshalls and Earl Warrens - have mixed a wise use of [the Chief Justice's] powers with a keen sense of diplomacy to move the Court in their preferred direction. But a key ingredient has always been the Chief's willingness to compromise his own views at times. This willingness is crucial, for it allows the Chief to create majorities that would not otherwise exist, and to prevent other justices from taking the court too far in the wrong direction.
  . . . .
  Such strategic compromise would hardly seem to be Thomas's strong suit. To the contrary, the evidence suggests that, unlike the most effective Chief Justices, Thomas may refuse to ever vote against his own sincerely-held views. To him, it seems, his vote must express his view completely and totally; it is not also sometimes a form of leverage to achieve the best long-term outcome.
  As Chief, Thomas would frequently face the unpalatable choice of either compromising his own views, or letting the real lawmaking at the Court fall to other justices. Either way, his influence would be muted. A Chief Justice who frequently writes alone - as Thomas seems bent on doing - and whose view of the law is idiosyncratic - as Thomas's plainly is - may be Chief in name only.
  In short, from the conservative perspective, it would be far more effective to keep Thomas as an associate justice.