Yup,
The issue is with those amoeba getting inside your body through an opening.... such as your nose, mouth, or ears. The Jet-ski, Parasailing, water mice, etc, while you may get wet, won't get you wet enough to risk your swallowing the water or giving those little critters the path to get thru those openings.
Not the mention that it's not like the lakes are infested with them and even touching the water means certain death. You could go swimming in the lake and be perfectly fine..... but since you are increasing the amount of water you are in contact with, and also submerging those openings within the water, you increase your odds. (and I'd also bet the above mentioned "kicking up the sediment" would be a factor too.)
That said... I'm still trying to figure out where I can get my Lake Snake Baked Cheesecake on a snack credit.