The John Ford movie with the best reputation that I don't really like is The Lost Patrol, but I've only seen it once. Also Arrowsmith was nominated for Best Picture and I don't like that one at all, but neither do any of the other 37 living people who have actually seen it.
Sticking to post-Stagecoach feature films, if there is one that I don't like it's What Price Glory. I haven't seen the Raoul Walsh original but it's supposed to be much better. The two from that era that I haven't seen are Tobacco Road and The Fugitive, both of which have uneven reputations. I remember when somebody on Dave Kehr's blog asked Joseph McBride (who at one point said The Quiet Man was his favorite movie, but didn't include it on his last AFI ballot, opting for Wagon Master as his Ford Pick) if he'd revised his negative opinion of Tobacco Road, and he said something like "I yield to nobody in my defense of Ford's humor, but that movie makes Green Acres look like Bresson."