Safety .. with the handle 1 you (the rider) can get caught in it, and 2 when tossing the rope into the boat, the large hard wakeboard handle has a greater change of hurting a passenger.
I think it is just a matter of preference. The knotted rope allows you more flexibility to pull yourself into the sweet spot on the wake. The shorter skinnier ropes with handles are also popular as they are lighter. Some people complain the knotted ropes are too heavy. Either way, use whatever you like, just don't use a wakeboard rope if and handle - use a wakesurf specific one whatever you choose.
About 4 years ago during a fall, my leg went through the handle all the way up to my thigh and flipped me over in the water really violently. That same season, a friend had the handle rip through her armpit in a fall, leaving road rash and bruising over the whole side of her body and arm.
I now use a short section of yellowjacket line, and an old braided ski handle that I cut the bar off of. I love it. You can actually see it in the pic I posted in the "best 99-02 wakesurf boat" thread.
It is definetly a preference. I have fell on the handle and burned up my armpit several times. Doesn't really hurt that bad and it gives you a good battle wound. LOL Wake surf ropes are heavy, and the knotted rope will also burn up your arm pit. We use a old handle from about 1970, and a skinny rope. works well. Buy a wake surf handle and use a skinny old rope if you have one. You are not going to hold it for long anyway.
I bought a thick (yet soft texture) rope from Home Depot and tied knots in it at various points. If I remember correctly it only came to about $15. It was one of those buy by the foot.
I like the rope better. It gives you the ability of being able to hold yourself at different lengths, and pulling yourself into the sweet spot. None of us have has a problem with the rope hurting a finger, or getting wrapped, etc. Even the girls!