It's a bit of a shame as they're a perfectly valid technique, and you can still do great things with them.
I loved that bit in Whedon's Astonishing X-Men where you see a scene play out and then later you see the same scene (with the exact same page of artwork) but with thought bubbles added to reveal a simultaneous psychic conversation that paints everything in a whole new light. (He used a similar technique in a Buffy episode).
I guess they're seen a bit as old hat and a relic of times past - possibly due to the way Lichtenstein used them and parodied their sometimes purple prose in paintings like this:
But it seems like their removal is just a fashion thing as much as anything else - part of showing that comics are a 'serious' art form. While putting thoughts in caption boxes instead of clouds does make some difference to the way you read them, I can't believe that thought bubbles are completely redundant these days. Hopefully they will be rediscovered to some extent in future.