As far as I know, upload does count against your usage. Look at the last column on the HughesNet Usage page.
I know it never has for me. But then, look at the upload speed! Mine is definitely above the "calculated" refresh rate, and I've often uploaded continuously for over 24 Hours to my clients. The upload speed is not as big a drag on the system as downloads.....well, maybe a verrry slow drain. -- HN7000S/PRO Plan/93W - 1039/.74m dish/1 watt