After some discussions I decided to test out if a protection filter degrades the image quality. I'm not planning to turn this into a technical blog, I just wanted to share my results.
A protection filter is basically a piece of "glas" that you put in front of your lens. It has no optical purpose as a UV-Filter or a Pol-Filter. It is used to prevent scratches on your front lens element.
I wanted to test whether a Protection Filter degrades Image Quality noticably or not. I tested two common situations:
Situation 1: No light on the Lens, typically when shooting with the lens hood.
Situation 2: A strong light to the Lens near the Subject, typically encountered when shooting outdoors with a low standing sun behind the subject. This creates lens-flare.
The test setup was quite simple:
I had the carpet hanging vertical. The shooting distance was 1.5m. The carpet was lit by a 580EXII at 1/128 power from below to enhance contrast.
Another Flash was used to create a lens flare.
Camera: EOS 50D
Lens: 100-400L and 25-105L (both canon) at 400mm/25mm
Filter: 77mm Protection Filter (also from canon)
Subject: A carpet
Flash 1: 580EXII aimed at the carpet, for illumination (allowing short exposure and low iso)
Flash 2: 480EXII aimed at the lens, for creating lens glare in some tests (Situation 2)
Settings: Iso 100, F 8.0, 1/200 s. I focused manually in all the tests with the magnified Live View.
Situation 1:

When looking at the picture top right, the contrast is a little bit higher than on the left with protection filter.
Both 100% crop are pretty soft, which is typically for this lens (they are still pretty sharp compared to other lenses!)
At 25mm the difference is even less, both 100% crops are very sharp, if you want to do some pixel peeping on your own, check out flickr.
Situation 2:

Here we have bigger differences, the additional element in front of the lens lowers the contrast. Especially at 400mm the difference is visible.
Conclusion:
It is safe to say that sharpness is not affected by the protection filter. The lens flare however is stronger with the protection filter. Under normal lightning conditions with a lens hood the difference are minimal.
Thus, I will continue to use my protection filters. It is clear that low quality protection filters shouldn't be used, as they degrade image quality considerably more.
All images are available on flickr in high resolutions. I suggest you take a look on your own if you are interested.