One name I keep hearing from the DC transportation world for Sec. of Transportation is Oregon Congressman Earl Blumenauer. He was an early Obama endorser and has done a lot of work on metropolitan transportation issues and infrastructure financing. His name was also discussed for this post in 2004, as I remember.
Earl is the genius from Oregon that put the bicycle reimbursement into the bailout package. He's truly a friend of cyclists and his potential to be Secretary of Transportation is truly an awesome thought.