You're probably right. There must have been some activity that drew the attention of law enforcement. It is a de facto obligation for cafés to offer free internet, so it's surprising to see such a law enforced in Grenoble of all places. My friend's café in Paris just has a password protected network, and I know for a fact they do not log traffic. I have seen other cafés with a registration system, and I'd bet those networks maintain logs. For the smaller cafés, even if they knew they had to, I'm not sure they would have the technical know-how to maintain logs. They've had some problems with piracy in the past, so perhaps that might have something to do with the arrests in Grenoble.

If torrenting or some other form of piracy happens on a network, ISPs send letters to that IP's customer, giving them a warning. Perhaps these café owners were repeatedly warned to enact stricter measures against piracy (i.e. logs), and, failing that, they were arrested for failing to comply with other regulations that are actually enforceable. I can't imagine a café owner could ever be charged with piracy for maintaining an open network.

For what it's worth, I looked around Le Monde and some other news sites to find more information, but there isn't much info to expand on the fact that these people were arrested.