They were legally compelled to add IP logging for that specific user. After this incidence, they went on to obtain a court ruling in Switzerland, where they operate, so that this specific attack cannot happen again. In their blog post about it [1], they instruct concerned users to access their account over Tor.

Of course when Proton say they don't log, we just have to take their word for it. People who don't want that element of trust can use Tor. Personally I believe their story in this case.

[1] https://proton.me/blog/climate-activist-arrest