Roberts, it seems safe to say, probably also voted against Obama in the presidential election. The chief justice declined to be interviewed in connection with the inauguration.
It won't be the first time that presidents and the chief justices who swore them into office have disagreed.
Marshall and Jefferson were political rivals who disagreed about the Supreme Court's role as the interpreter of and highest authority on the Constitution. Marshall claimed that power for the court in the case of Marbury v. Madison in 1803.
Chief Justice Earl Warren and President Richard Nixon both were California Republicans, but Nixon campaigned for president in 1968 in part against what he saw as the liberal excesses of the Warren court.
Nixon's inauguration in 1969 was the fourth and final one for Warren as chief justice. It was also, in the words of Warren biographer Jim Newton, "surely Warren's least pleasant trip to that podium."