I know that oftentimes venues take a cut of the merch. Amphitheaters and arenas take pretty hefty cuts, which is what I think helped lead to the $35 standard we see at those places. I even remember the Key Club demanding as much as 30% back when it was still open. Ravenheart pretty much nailed it on the head though.
More often than not, shirts that are $15 or less mean that the band is really fricken rich and is willing to take a loss for the fans' or their image's sake (Foo Fighters), they've reduced their overhead enough and/or control the market (Bolt Thrower), are trying to unload stock that no one wants (Impaled), or are a small band willing to take a loss in exchange for spreading the brand and gaining some free advertising (Funeral Age).