Jagman1,
take a quick look back at some of the people who've been cat B'd over the last 8 years. Quite clearly the vast majority of those decisions by the star chamber were purely political. Intimidation is the only word to describe it. So, in a small way, bypass pay provides some minor compensation to those victims.
Regarding the slightly more difficult question of pilots who've failed command course, and are awaiting re-assessment, some (but not all) have been subject to some strange egos in the C&T department. We all know that it's a big HILL to climb to achieve you 4BARS. (a couple of big hints in there!) Where do you propose that we draw the line?