I prefer not to, as it tends to scare them. I imagine it feels a bit like a predator swooping down and grabbing them.
I've also noticed that several of my adopted/rescued rabbits are very sensitive around the neck/shoulder area, and I know others who have noticed this with theirs. Usually these rabbits come from a place where they were routinely scruffed. For example, the shelter workers at the place I got Loki routinely scruff rabbits. They know how to do it properly, but he spooked whenever I touched his neck for months until he learned I wasn't going to do that.
It's also not a good idea to scruff large rabbits. Even with properly supported hindquarters, it's very uncomfortable to have that much weight put on the skin.
I much prefer to just slip one hand under the chest and one under the butt, then lift. My previously scruffed and hand-shy rabbits have learned to find this acceptable and don't usually fuss too much once they're used to the idea.