JackM,
http://www.biosecurity.govt.nz/pest-and-disease-response/pests-and-diseases-watchlist/didymosphenia-geminata/science-technical
http://www.epa.gov/region8/water/didymosphenia/White%20Paper%20Jan%202007.pdf
I don't know that the specific source for any stream containing didymo has been identified, but there's plenty of studies which looked at the suvival of didymo under various conditions. Basically, a single drop of water can contaminate an entire waterway system, but dryness, detergents, etc. kill it. It cannot be spread in the intestines of birds or bugs, though I would think ducks and geese, in the feathers, could spread the stuff. It can be spread on boats, swimmers, cars, wading gear, washing infected gear down storm drains, etc. It can live, but does not thrive in strongly alkaline waters, so limestoners can get it but would probably be less affected --> its less likely to be reported there. Beyond that, it seems to be turning up primarily on the "destination" freestone fly fishing waters, the very type that the avid fly fishermen with money to burn take frequent trips to. Gunpowder, White River, Connecticut River, Battenkill, upper Delaware, White River (Arkansas), many western rivers, and several New Zealand streams. From the list of streams affected, I think its pretty clear fishermen are the #1 transportation vector.
The fact that it can be transferred by a single drop of water means that basically anything can transfer it. If you hop river to river, you are a potential vector, your waders, your skin, your clothes. But complete drying does kill the stuff. The reason felts are picked out is because the interior of the felt can stay moist for months, and studies have showed that didymo can survive in felt for 2 months or more. So, if you like to travel to fish, so long as you dry your waders between changing streams, you're ok. But your boots, you'll need to put them in water held above 140 degrees for a half hour, freeze em solid, or use bleach or detergent and let soak for at least a half hour. The only other choice is to have a different pair of boots for each stream, or give them at least 2-3 months before wearing them in a different stream.