GoJets is on the reciprocate list of almost all other legacy/major/regionals, so you will not have any issue. Anyone with a small male size organ decides to give you hard time and denies you, thank them, but make sure you note their name, airline, flight number, and date, and then go through your jumpseat coordinator to get to the bottom of it. I guarantee you that pilot will be getting a call from one of his jumpseat committee members asking more about the situation. Jumpseat wars against GoJets are mostly online forum tough talk, you shouldn't have any issue on the line in real life.

As for GoJets on your resume, no one in airline HR cares about regional pilot squabbles! For that matter, most major airline pilots don't keep up to date with that stuff either. All that matters is the flight time and quality on your resume. GoJet pilots have left to move onto legacies and majors. I know one who went to Fedex and a couple at VX too, Spirit, and JetBlue.