Yeah, that usually is the problem. The fact that many people from the western world are unfamiliar with Islam and Muslims, makes them an easier pray to the immense propaganda they are exposed to.
The idea is like this, each country in the world is or should be trying to make a system that reflects the values that this society holds, and protect minorities living in that society and so on.
For a country that contains a majority of Muslims, their values are driven from Islam, so naturally, their system should be so as well. That however, doesn't mean that non-Muslims in the community should be 2nd class citizens, or that they should be exposed to any oppression from the religion.
The fact that governments and leaders in general are most of the times corrupt and/or incompetent is the reason for why minorities are usually oppressed.