I live in a wine-growing town only about 20 miles from Rüdesheim. Rüdesheim is a very 'touristy' place, but in September it should start to get a little quieter. The weather can be very pleasant at that time of the year. You don't say when in Septmeber you will be there, but a number of wine cellars have open weekends when you can get an impression of how they work and, of course, sample their wines. There's one in Eltville from the 9th to the 11th, for example, and another the same weekend in Oestrich-Winkel. Both places are not far from Rüdesheim. Then, there's 'Rhine in Flames' fireworks spectacular in Oberwesel, also on the 9th. Most of the wine fests are over by September, but there is one in Boppard on the 22nd to the 25th.
I'd recommend driving along the Moselle on your way to the Rhine. I think that route is as pretty as the Rhine between Koblenz and Mainz, so you can double the enjoyment by going that way.