I'm not sure that all applies here, but "Marcel the Shell" obviously belongs to and is associated with one specific brand, and the author of this nix shell is riding on that. It's not like when someone tries to trademark "Apple" in 2 different contexts.
A trademark claim here might not be dismissed under Rogers, but I don't think there is any jury that could ever find that consumers were likely to become confused about whether or not the command line tool Marcel the Shell was affiliated with the independent film cartoon character, and even if that could be established, unlike Jack Daniels, what $$$ damages were caused in trademark dilution? 3 figures?
It's more or less the same spirit as the Roddenberry estate allows someone to use the names - you are allowed to build a warp drive, as long as it warps spacetime and allows FTL travel.