The difference is, Baseball has been granted, by Congress, a special exemption from normal anti-trust rules. In trade for that MLB must endure a level of Federal scrutiny not tolerated by other sports.
What Congress has to do investigating steroid use in cycling is beyond me. Notice however that once they stripped Armstrong of his TdF wins, they did not award them to anyone farther down the list. Why? Because Armstrong was riding on a level playing field; everyone was juicing, the entire field. They just wanted to clean up the sport and the best way was to come hammer down the nail that was sticking up.