It's both. I don't know why this point has to be rehashed, although I suppose it does bring into focus why speech railing against a *race* might be treated differently than speech railing against a *religion*.
You should be able to criticize anybody's beliefs. And not be violently or forcibly suppressed by the state in doing so.
But there is comparatively little social utility in criticizing people *because they are identified as part of a group, irrespective of their personal beliefs*. This is because individual character, and individual beliefs, are the point. Judaism includes both religious beliefs *and* identification as members of an ethnic/racial group, regardless of what the religious beliefs of the person happen to be.
If that's too abstract, consider it this way -- when the SS came to your door, it was no answer for you to convincingly show that you are an atheist who spits on the Judaic religion. If you were identified as a 'Jew,' that was the end of it. The SS had not the slightest interest in Judaism as a religion. It was Jews they were concerned with, as an ineradicable ethnic and racial identity. Now it's certainly a vague and variable ethnic/racial identity, no questions there. But it's something that people are stuck with, regardless of their beliefs.
There are tons of atheist Jews. Israel itself was originally built for atheist Jews. There is as of yet, however, no 'atheist Muslim,' any more than there are 'atheist Christians.' The essence of the identity remains belief, such that if you have the belief you are the identity, and if you don't have it, you aren't.
And even if that were the case, it's no more legal in France to incite hatred against Muslims than it is to incite hatred against Jews. There are tons of prosecutions for both. Hate speech laws are primarily used as a hammer against the far Right, including anti-immigrant speech.