<Why cant someone use a boat to run?>
Rule 5 says...
5. All vessels must be man-powered (no motors).
That pretty much rules out a boat for running, unless it's a row boat :P

"Man-powered" is the entire point of one of these tournaments. That's what float tubing and kick boating are all about.
It's about the competetion between men(and women) and the fish. Using the tools you have, within the rules. Man-powered!

<Whats the difference in what you drive from 1 spot to another if your running?>
I think a boat, if allowed, would provide an unfair advantage over those who don't have one at their disposal. Big difference!

<Like the way running is currently done all fishing would be out of the kickboat or tube. What's the difference?>
The difference would be the time it takes to get to a location. For example, at Clear lake you launch at state park and want to run to Quercus point. Boat time, less than 5 minutes. Rowing a kickboat from state park, 45 minutes to an hour. Driving to county park launching kickboat and rowing, 40 to 50 minutes. These times are just educated guesses but you can see the advantage running in a boat would have.

my .02
MT