Dream Theater is a popular group, not because they get a lot of airtime on the radio but because they tour a lot and gather fans that appreciate their heavy and driving music and/or have enough musical knowledge to truly appreciate the incredible technical talent of the players, the intricate time changes and arrangements, the humanly relatable lyrical content as well as the overall feel of the music.
It is no surprise that when nominated for a grammy award they lose to the Foo Fighters. Arguably the FF don't even belong in the category, but they are a very popular band that gets a lot of air time. In general people have very simplistic views of music and the blatant superiority of the music of DT is something that they simply do not have the sophistication to recognize.
The Grammy awards are generally pop musicans patting each other on the back and convincing each other that they did a good job. It would be nifty if DT got the recognition too, but everyone familiar with them just knows, and a plaque or statue or pen and pencil set or whatever their trophy is does not change that knowing.