I’ve had mine for roughly a year and a half, and while not a panacea for all logistical problems inherent in rafting, it is certainly a huge plus.
I too was at first worried about purposely putting a giant hole in my boat, but with some alterations to setup, it can be really, really, really nice. The main stumbling block i’ve found is making sure that anything I might need on the water isn’t in the tubes because having to open it really slows you down (having to re-inflate your boat etc), but with a bowbag or a drybag clipped behind my seat (I’m 6’ with a llama with thigh straps and my seat is moved forward about 6"), i find that having the day’s stuff accessible is easy enough. Having paddled with non cargo-flyers, I will say that getting onto and off of the water takes a little more time, as you have to unload and reload your pack every time, but if your pack is organized (or better yet you pack everything into the provided drybags), its not bad. As to sand, I was rafting in Montana this summer and a lot of the rivers I was on were either sandy or gritty and I had no problem with a poor seal; the zipper got dirty but it didn’t seem to leak.
Overall, if money isn’t an issue and you want to shoot whitewater with a big bag of stuff or a bike, get the cargo fly, hands down.