I never actually watched the ending to Dinosaurs, and the first time I learned of it was on Cracked (I somehow missed it, go figure), but while it does strike me as the most depressing ending to any show I know of, it also strikes me as entirely fitting.
Light-hearted show? Yes, but it was also a show with heavy social commentary. From sexual harrassment to mocking our dependency on television to the deplorable use of religion as a tool to make money, Dinosaurs used all those animatronics to make a point or two. Sometimes the best way to get under people's defenses is to trick them into believing they're watching something harmless.
I rememeber an old Disney cartoon based on the Chicken Little story, where a clever fox uses rumors, mass hysteria, and a guilible sap (Chicken "the sky is falling" Little) to steer an entire farm's worth of fowl into a cave, where he planned on devouring them at his leisure.
Do they escape? No. The fox won and kills them all (yeesh, it was a dark ending for a Disney cartoon). The point of the cartoon was to teach a moral about the dangers of rumors and getting caught up in panic and fear. It was there to teach us a lesson, not the characters.
Dinosaurs was the same way. The ending was to remind US of our potential future, not the dinosaurs. Pretty brave, I'd say.