I've always just sat my children down and done them. Never had a problem with it. My best friend back in Virginia couldn't believe that they would sit still long enough to have them done without pitching a fit, especially as her daughter, who is the same age as my son, would scream bloody murder anytime she mentioned clipping nails. But her daughter would let me clip them no problem. lol After we found that out I would be the one to clip her nails. I don't know what I did differently than my friend, though.
My daughter has rarely had any issues either! I wonder if kids can sense their parent's hesitation and that makes them nervous? I know some parents can get really nervous about cutting nails. I did at first too and just got more confident as she got older. I think hubby did it at first too, using one of my clippers or something but we also used her baby clippers (I never used the magnifying glass though, that made it MORE difficult). I would just push her finger back a little to expose more of the nail, put the clipper part where the nail was and cut. I've had very few issues with cutting them or getting DD to hold still to have them cut. And now, I cut them pretty frequently, pretty much as soon as they start to scratch me I cut them.