Under 10.7, when you use the Red "traffic light" button to close all windows of an Application, it appears to quit. This is a new feature, ported from IOS, the land of tiny screens and no backing store to ease the re-launching of Applications.
Actually, the Application is likely to still be running in the Background, and will really quit only when memory gets low.
If you want to Quit Applications with Command-Q under 10.7 and later, you need to do so when at least one Applicaton window is still open. Otherwise, you get the behavior I described above.