Rover,
A lot of the old timers and commercial product manufacturers recommend cotton based on the fact:
1. They've used cotton for years and don't have a problem with it so why change a good thing?
2. Quality Control Issue: MF is a new technology and it's just now starting to gain momentum in North America. There are many more poor brands out there than good ones. Where as, 100% cotton is much easier to find and you don't really have to worry about QC.
If a Meguiar's was to go out and recommend Microfiber without stating which top 3 or 4 brands we recommend (JT, Paksak etc.), they run the risk of someone using poor quality MF and scratching their paint and holding the company liable. Also, bad PR that could ensue.
Sal himself has said he has tested many many brands of Microfiber and still recommends 100% USA Cotton towels because there were only a couple of good Microfiber manufacturers and didn't want to recommend any one vendor over the other.
Lastly, old school thinking. Hell, some people still recommend washing your car with dish detergent every wash. Then there's the whole pledge use etc.
Don't lose sight of the fact that avid enthusists like the people here account for probably less than 1% of the total population that maintain there cars. Which is less than 25% of the people of who owns cars.
We're definitely an extreme minority for Companies like Meguiars, 3M etc.