You can protest anything or be protested for anything. That does not mean you will win or lose in the room. But I beleive the onus is on the port boat to prove that it did not cause the starboard boat to take corrective actions. So if your are going to cross make sure that it will be clean. Not just the way you look at it but also from the perspective of the starboard boat.
As stated before the rules are to be honored. That goes for both the boats. Calling protest should only be used when you HONESTLY feel you have been fouled. And calling Protest when there obviously was no foul is not honoring the rules.