The main downside I found in connecting fans to the peripheral cables instead of the motherboard is you lose the ability to have your motherboard in control of the fan. That's assuming your motherboard has controls for fans in the first place. That's why some people will invest in fan controllers. You can hook your fans to it, then control the fans from there, without involving your motherboard at all.
Some fans operate at 100% speed if directly connected to the power supply cables. That makes the computer noisy. It's nice to be able to set fan speed to whatever you want, so when you want quiet you get quiet.