you need to use spray mount and mylar (or aluminium foil if youre cheap) to Blackout the pipe. root rot needs light to grow, but not very much. absolute darkness keeps it from growing.
also more flow of cooler water will help keep it in check, as well as just a few drops of hydrogen peroxide in your reservoir (2 tsp/gallon would do)
theres lots of stuff out there, like silicone root solutions (they apparently work well though i never used em yet) but in a hydro system you gotta peep at your roots regularly and if your plants start having issues thats the first thing to check .
to sum up:
use spray glue and mylar to completely wrap the pipe (or switch to black abs pipe which is cheaper and comes in bigger diameters)
check your roots at least once a week or when you change your rez (every plant)
cooler water temps (but not cold, not even chilly!) and hydrogen peroxide in moderation
more water flow.