Logan is the only one who can be around Charles thanks to his healing powers. The rest of the X-Men can't be in close proximity near him, so I wouldn't say they abandoned him, Logan is just taking responsibility and taking care of him.
Before anyone says what about Jean, sure I guess. But this film is about Logan.
I would like it if they had the Shi'ar depower Jean like in the original ending of The Dark Phoenix. That would be able to explain why she was helpless.