A big market can actually be a bad thing, particularly if competition from pro sports comes with it. Quite a few programs have to deal with being in the NFL's shadow:

NE Patriots: BC (and to an extent UConn & UMass)
NY Jets/Giants: Rutgers
Buffalo Bills: Syracuse (could have more regional appeal)
Philadelphia Eagles: Temple
Pittsburgh Steelers: Pitt
Washington Redskins: Maryland
Cincinnati Bengals: Cincinnati (Bearcats, that is)
Chicago: Northwestern
Carolina Panthers: Charlotte 49ers and probably has some impact on all the Carolina teams
Atlanta Falcons: GT, GA St
Tennessee Titans: Vanderbilt
Tampa Bay Buccaneers: USF
Miami Dolphins: U of Miami, FAU, FIU
NO Saints: Tulane
Houston Texans: Houston Cougars, Rice
Dallas Cowboys: SMU, TCU, UNT
Minnesota Vikings: Minnesota Golden Gophers
Arizona Cardinals: Ariz St
Seattle Seahawks: Washington
SF 49ers/Oakland Raiders: Cal, Stanford

I left off the LA teams because I feel like they have done just fine even when they shared the market with the NFL but I with its return I think the brand names of USC and UCLA will remain strong.

Many of those programs were much better supported within their cities before the NFL grew in popularity and expanded through the 60s and 70s.