Good question. One that I dealt with myself a short time ago. My recording are made with the InfiniTV card card recorder, and many are marked as protected.
Start the Processing Condition Editor that is part of the dvrms toolbox suite of programs. Then add a new condition. Give it a name like "Don't mess with protected files" and then add a condition by clicking the 'add' button. Choose WM/WMRVContentProtectedPercent, select greater than and add 0.
Then choose a profile from the drop down list to run when you've got a copy protected file. I made a custom one that just renames the file creates a 'fake' commercials file and ends.
The reason you have to use the percent and not the yes/no is for some reason, some recordings are not flagged correctly, but the percentage is always correct.
Using this method I'vehad 100% success for months now.