August abandoned Emma for most of her life, when he was meant to look after her. That scene in The Stranger where he goes to Marco’s shop, and he spells out what an EPIC FAIL he’s been and how his father wouldn’t be proud of him, shows that he’s ashamed of his actions. Yes, Marco said that if he had a son, that stuff wouldn’t matter to him, but now that Marco remembers who he is, August may think that his opinion of him would have changed, so he may not be able to face him.
Also, there’s the whole deal with how Geppetto made Blue lie to the Charmings about the tree only taking one. There are lots of fans who want Geppetto to have to answer for that. Maybe August would feel that by hiding out, he’d be protecting his father from the truth coming out.