I must have done something wrong. When I am using the QGLWidget as a QMdiArea Subwindows it works fine (it always has the full size of the subwindow and I can resize and maximize it).
By adding a QMenu to my QGLWidget and set it as viewport it seems that just the QMenu is drawn. Is there any difference between a widget used in a subwindow and one used as a viewport? For me it looks like the QGLWidget does not take its space by the default when it is set as a viewport, when I am using a different Widget, such as the QTableWidget it'll take as much space as needed.