Go to manage applications and uninstall it just like any other application. Since you did a factory reset you should have lost root so uninstalling superuser should not cause you any problems. You can even go to the market and search for it there and uninstall it.
But it depends if you have clock work mod installed. If your phone is back to factory original state then it is safe to uninstall super user
Then you need to root your phone again. Then before you do a factory reset unroot your phone properly. After that you can uninstall the Superuser app or do a factory reset.
Seeing as how this thread is about troubleshooting a root-only app, I'm going to go ahead and move it to the ROMs/Hacks sub-forum. In that section you can also find the How to Root thread. Happy rooting!
The first post there has instructions on how to unroot but I will post them here too just in case you dont feel like going to that thread. I would advise you too anyways so you can see the big picture.
How To Remove Root
adb shell
su (its going to ask you for permission on your phone so hit allow)
mount -t rfs -o remount,rw /dev/block/stl9 /system
rm /system/app/Superuser.apk
rm /system/xbin/busybox
rm /system/xbin/su
rm /system/bin/su
rm /system/bin/busybox
mount -t rfs -o remount,ro /dev/block/stl9 /system
exit