Most college and pro teams don't care if high schools are using their logo. The high schools aren't making any money off of it and it's basically free advertising for them. Here are some more I can think of in MS.
Water Valley-- West Virginia
Brookhaven High- Ole Miss
Hancock High- Philadelphia Eagles
Starkville Academy baseball hat logo-- Arizona State
Brookhaven Academy-- Kansas State
Wayne County- Auburn
Hattiesburg High- LSU
Purvis-- LSU
Starkville High- Georgia Tech
Desoto Central- Washington Nationals
They have started caring quite a bit, because there is now big money to be made in logo sales, and policing unauthorized uses has become much easier. Also, for the majority of colleges that have signed on with Collegiate Licensing, there is an outside agency that will do all the policing for you.
If you knowingly allow other teams to use your logo, then you risk losing the right to enforce your trademark rights against unauthorized users. A nominal license seems like an easy enough solution, but there are a couple of problems. First, with any trademark license you have to retain the right of control in the quality of the goods produced. So, an NFL team would have to have a team of quality control experts out there monitoring the various pieces of crap that high schools like to adorn with their logos and possibly put a stop to the more ridiculous uses. Second, a really cheap license could be used as evidence that your trademark is not worth very much, or that the license is really just a sham. Lots of problems there.
If you notice, a lot of NFL teams have come out with new logos in the past few years, and they aren't licensing those logos to high school teams anymore. Several high school teams used to use the old Patriots logo of the dude hiking a football, but I don't see any using the new logo (and I'm still not really sure what that logo is).
