People were not hip to Eli because he's not the fiery jumping bean that his brother is.
I think people read Eli as being a bit aloof and sort of uninterested in being the best.
Funny thing is that he's achieving championships and cranking out season after season as a competent QB, and people still say things like "Tony Romo is underrated. Really, Romo is a great QB who just doesn't have the pieces around him..." LOL. Seriously, that people bag on Eli and exalt Romo (not saying in any way I'm targeting posters here, just making general statement) its utterly laughable.
My dad is a lifer for the Cowboys, and he seriously has a deep rooted hatred for Eli Manning. I think it's partly his past dislike for Archie...but there's some QB envy going on too. If Eli was leading the Cowbabies to Super Bowl titles, my dad would be the biggest Eli fan in Texas.