Yes, they did make fun of Judaism alone from time to time, but not nearly as much as Christianity. A good example of what you could find in it (translation: title "circumcise all males the eighth following their birth"; commentator: "why do we not wait for him to be old enough to understand?"; rabbi: "we have to enjoy our superiority while we still have it!").
Here is an article (in French, but English speakers can get the gist) including statistics on their front covers. The overwhelming majority is about French politicians, and their favourite religious target is the Catholic church. Usually, a rabbi is present when they decide to make fun of religions altogether.
There was legal action from LICRA (International League against Racism and Antisemitism) in 2008 against one of their journalists on antisemitism charges. It was not against the paper itself, though, but about some things the journalist said on the radio (more here).
The religions they make fun of are kind of correlated with the religious profile of France. Since they mostly tackle current affairs, one can also assume they make more fun of the noisiest people. The Jewish community in France, even though it is the largest in Europe, is still only around one percent of the general population (I say "around" since religious profiling is forbidden in France, all you can get are rough estimates).
If you want to know more about who Charlie Hebdo pissed off, their website has a special court section.