Roberts filled the vacancy left by Rhenquist, hence why Roberts is CJ. Alito is going to fill the vacancy of the outgoing O'Connor who is leaving for personal family reasons.
Who they were nominated for and who they actually replaced got switched when Rhenquist died. We're all correct. :-)
I thought that Roberts was chosen for CJ in his own right. If Renquist hadn't died, he would have taken O'Conner's place and when he died, Bush would have still made him CJ. Am I off base?