In all the "I am Charlie" upheaval about the attacks in Paris one can also sometimes hear a countervoice. That is a voice that says that "they had it coming" by insulting 1.6 billion Muslims in the core of their existence: you need only one madman who doesn't suffer in silence but takes action.
These approaches come from different cultural backgrounds. Those countervoices come from societies where religions live in mutual respect. They have the assumption that society is static and that people will die in the religion in which they were born. In such an environment religion is something like the color of your skin: it is a part of your identity and as such it should be respected. Atheists who want to denounce their former religion will find that their freedom to do so is severely restricted.
However, religion is not just a passive identity. It can be very active, both trying to recruit converts and to impose its vision on society. In that form religion looks a lot like ideologies and for ideologies we don't have this kind of respect. We don't mind people accusing communism of enslaving people or neoliberalism of stealing from the poor to give to the rich. We may not agree but we believe it is essential free speech. In this context we know the borders between free speech and respect. We may not agree with our communist neighbor or colleague but we will not use our arguments in a way that humiliates them. We still respect them as a human.
Similarly we usually know the limits of joking about religion. There are much more jokes about the "foot between the door" of the proselytizing Jehovah Witnesses than about the Virginal Birth because the first is an active "ideological" point while the latter is a basic part of the belief without consequences for non-believers.
Jihadi's are by excellence Muslims with an activist "ideological" agenda. Often they actively seek points of difference so that they can achieve small victories. See for example "Islamic banking" that was invented as an ideological statement yet has no long long history within Islam. In this context Charlie Hebdo's criticism of Islamist extremism is fully justified.