His comment could also be implying that he thinks you are a JV-level official. Hey, I've been called worse things , especially on a baseball field
If he had said the comment in a normal speaking voice I would've ignored him. Since he yelled the comments I would've probably said something about playing with the same FED rules at the JV level as the varsity level. Tell him it's a travel there too.
If he chooses to throw a water bottle, that's not your problem.
I was calling a game in PA about 10 years ago where a coach (who is also a college football official, BTW) got so mad at his team he slammed a clipboard to the floor whereupon the "clip" part shot out across the floor right in front of me. T. Sheepish look. Once coaches throw things, well, they're responsible for what they throw.
Rich