In general the state of colorado would have the first tier of authority for regulating motorized water craft on rivers. According to the colorado state parks folks, the arkansas river from the headwaters to pueblo reservoir is the only section of river in colorado that the state specifically bans motorized water craft on. Don't have a link, but got this from the state parks boating coordinator.
Aside from state regs, other agencies that regulate the land rivers flow through can have their own regulations (blm, municipalities, forest service etc), although its seems that most don't. The BLM noted that there were no BLM regulations prohibiting motorized water craft in colorado that they were aware of.
It seems that the city of glenwood springs does have an municipal ordinance banning the use of motorized water craft on the colorado and roaring fork rivers within city limits, so jet skis at the playwave in town are illegal, not sure if south canyon wave is outside of city limits or not. See link below.
As for motorized craft on rivers, rafts freqently use motors on flatwater, jet boats have been around for many years on rivers, and jet skis have been used as well. Jet boats are commonly used in idaho for shuttles and river trips. Motorized water craft are used up and down the colorado river, even through the grand canyon.
As for the negativity towards motorized users... I personally have no ill feelings, although I primarily kayak. I know where to go if I want a pristine wilderness trip, and most of the time, my group is the only group within eyesight on the water. I also know to expect lots of other river users in popular locations, and realize that I'm not the only one entitled to use the river. In the spring and summer, most folks love the water, and its there for all of us to use as we see fit. I do think it makes sense to have some common sense and keep fast moving motorized traffic like jet skis a safe distance from other boats, but thats another story.