You don't see why context matters? Sure, Jeff and Vinny would look back and probably be like "ugh, those are some dumb jokes we made", but that doesn't mean they were terrible people back when they made those jokes like they would be considered now if they made those same jokes because they were normal jokes that everybody made.
To get back to Yosuke, he's literally the average mid-2000s high school dude. Is it really a problematic portrayal if it's an accurate portrayal? In reality, the odd thing about Persona 4's portrayal of mid-2000s high school kids is that everyone except Yosuke is so tolerant. Yosuke's not inherently this horrible person because he's nervous around someone he thinks is gay or makes gay jokes or thinks cross-dressing is gross. Hell, until Cam'ron made it popular, teen boys during that time were terrified of just wearing pink. Ironically, Cam'ron was also responsible for an extremely common gay joke back then.