I think it is perfectly rational to believe that one set of protests support a bad or unimportant cause and another support an important and good cause, and thus judge that one set of protests is justified despite the risks, while another is not justified. Why would this be an irrational/hypocritical position to take?

Of course, the belief in the importance or validity even of the causes of either protest can vary between people, so various people may support none, one or both protests, according to their particular beliefs. I wouldn't call any of these people irrational (though of course I have my own beliefs and only agree with one of these positions).