After it was asked through the HITS Formspring I got really curious as to what the deal is with all of that stuff.  So I went to Tally Hall's manager at The Hornblow Group and asked about it. His answer couldn't have done a better job explaining it so I will quote him here:
"If it were easy to license your music to Rock Band, Guitar Hero, etc. Tally Hall would have done it. However, there are many factors at play on the business end (e.g. sales estimates by the company, cost to license the song, cost to create/program the song, how familiar they believe gamers are with the artist).  In cases where they don't come to the band, it's a matter of the label (Atlantic) or publisher (Tally Hall) getting strong on them. Hornblow has licensed tracks for other artists for games of that sort, and believe you me the amount they pay isn't much, nor does the exposure amount to much.  But that isn't to say the band would decline if ever offered."
I have also been informed by a fan through Twitter of a thing called The Rock Band Network.  Harmonix sends a kit to the artist who then maps their songs for the game.  I'm guessing this could at least get their songs available for purchase through the game's online store, but not part of the game's official track list (better than nothing, though!).  Plus, with all the business side of things we just learned about, it might be easier for indie bands than it is for signed bands to do such a thing.