Various things
I prefer cubase for a few reasons...
first of all I am simply more used to it an resist change
There is also the matter of hardware and software lockin when you use digidesign (as you mentioned), which I find very oppressive.
Also, the lack of automatic delay compensation in protools LE is a deal breaker for me...
Regardless of whether you can afford an HD system, many people like to keep a smaller portable rig for convenience when remote recording, and I resent the idea of paying for intentionally handicapped software. (let's face it pretty much every other recording app has it, across all price levels)
Finally, While audio recording is quite usable and featureful in cubase (Once you learn it that is), midi in protools is just abysmal.
In fairness, there is one feature I find cubase to be sorely lacking though: side-chaining. I hear this has been added with VST 3 in cubase 4 though.