Is targeting "ideas rooted in fascism or bigotry" a bad thing?
The root of the problem is that it is basically impossible to defend yourself against the accusation that you are secretly a fascist. If you say yes, you admit to being a fascist, if you say no, you're a lying fascist. If you question why the accusation is levied against someone else, you're defending a fascist, if you speak out against the proceedings, you're defending fascism.
The only way to prevent accusations of harboring secret fascist sympathies is to deflect the accusation by lashing out against others with the same sort of accusation, thus demonstrating that you are not secretly a fascist.
This is a dynamic that has repeated itself many times, it's the engine behind countless actual witch hunts, but also metaphorical ones such as the McCarthy-era red scare, the ideological persecution under Stalin.
The PATRIOT Act is a terrible law. Opposing it doesn't make you a terrorist. But you would've been accused of being one nonetheless if you opposed it in 2001.
It's easy to see why many people wouldn't want to actively get into such a controversy. But even that is being used as grounds for kicking someone out.