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.
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?
Plenty of books, films, and TV shows have the same titles, which indicates that titles alone typically don't enjoy the protection of exclusivity.
Copyrighted characters and trademarks have a better chance of that, but those aren't being appropriated here, just the name.
"Marcel" is also a common first name, which makes it less likely that the creators of the film can claim any exclusive use of it, and "the Shell" is completely descriptive in this context, so unlikely to cause copyright issues.