In 2004, Bush's party won four seats.
In 1996, Clinton's party lost two.
In 1984, Reagan's party lost two.
In 1964, Johnson's party gained two.
In 1956, neither party gained.
In 1948, Truman's party gained nine.
In 1944, FDR's party lost one.
In 1936, FDR's party gained five.
This amounts to an average gain of one seat.
These results tell me that there isn't really any apparent trend to be found here, or any hint of what we can expect should Obama win in 2012.
To answer the question: Yes, there is a very real possibility that Obama could win re-election while the GOP takes control of the Senate.