Assuming he isn't impeached and removed first or that he decides not to run, you are right that he will be the nominee. BUT, that's not the end all be all.
When you are the incumbent and you have at least one serious challenger in your own party in the primary:
1) Shows some disapproval in the party about your governing.
2) Gives a voice to that candidate about how bad the incumbent is that will be listened to by some in the party who would just ignore negatives from the opposing party.
3) Makes the incumbent spend time and money fighting the in-party challenger when they'd rather focus on the other party.
4) It is one of the 13 keys that is against the incumbent.