Nah, I'd have Atherton ahead fairly comfortably TBH.
Both good batsmen, and certainly better than Matthew Hayden, but Hussain did the job for, in essence, 6 years, and had 1 absolutely horrible year (for no particularly good reason) in the middle of this. Atherton did it for 10, and was ruled-out\completely-useless due to injury for just over 1 of that. Basically, it's Atherton 9, Hussain 6.
Atherton was technically better, obviously, and was also better at cashing-in on weak attacks and flat pitches. Hussain was brilliant, absolutely brilliant, when there was something in the pitch for good bowlers, but because of his mindset - fear of failure was always huge - he never cashed-in to anything like the extent he could have when the going was easier. Atherton was pretty comparable against powerful bowling, and though Hussain played less against the likes of Ambrose, McGrath and Walsh so had less opportunity to be dismissed by them, I'd probably just, and only just prefer him. But even in Atherton and early on in Hussain's day, there were weak attacks from time to time, and Atherton was much better at cashing-in on them.
A far more interesting "vs" than many of late, though.