It's not blaming all Muslims for the actions of a few. It's that the religion that they follow doesn't condemn the actions of the few.

Christians don't agree with each other on everything, but a majority of Christians, including scholars and clergy have denounced the Westboro Baptist Church for their evil behavior. They made it very clear that the WBC was an extremist sect, and they they are not accepted by the rest of the Christian community.

At the end of the day, the Islamic Republic of Iran is using their religion as their justification for their evil actions, specifically regarding the oppression of women and members of the LGBTQ+ community. What they are doing is evil and morally abhorrent. The question has to be asked, are they evil people twisting their religion to fit their agenda, or does their religion actually promote that kind of behavior. That mostly has to do with how the rest of that religion's followers view those actions. If Muslims and Muslim religious leaders come out openly condemning the actions of Iran's government, pointing out how their actions go against their tenets, then great, we treat Iran as a group of extremists. But if Muslims and Muslim religious leaders don't speak out, it's because they think what Iran is doing is morally acceptable, or even preferable.