I have only played a JC through Act I of the story, so I freely admit to not having the full picture but I do have some thoughts about this.
The JC storyline, at least in Act I, is about sacrifice. Your character gives up their own strength and power to shield others and is "weaker" as a result. A lot of players don't want or like that; they want to be the strongest they can be. A lot of them, and I'm going to be biased here and say that this is particularly true of those who play Sith for the most part, do not understand the idea of sacrificing for another. They'd just want to kill the infected Masters and show how bad *** awesome they are. It challenges the typical MMO approach/story of getting to be uber-strong and just smashing your way through whatever the danger is. At least for most of it, the threat is one you can't fight directly and that turns off a lot of people too.
There's also an aspect of redemption; the corrupted masters have done some bad things and many players feel they should be "punishing" them (back to the killing thing above) rather than healing them.
I may be off on that, but that's what I've taken away from people talking about this in General or even in other parts of the forums.
QFT. Especially if you are a Shadow and playing your character as a type of Jedi Order enforcer, having the story force you into a healer self sacrificing diplomat can be off putting, not to mention the story just doesn't feel as epic.
And for me it wasn't that I wanted to just smash everything as more playing a Shadow which I saw as more a role within the order to carry out some of the secret and dark missions and thus I didn't feel the idea of being some talk it through diplomat healing others type fit my character.
Kind of the same reason I get sick of not finding pants to wear on the light armor force user classes. We aren't all playing these to be some behind the lines healer in a dress.