I watched the video (1x) and because of the (lack) of the quality of the video at the beginning I can't definitively make a judgement as to whether the two "breakaway" riders on the training ride for sure saw the standing cop motioning and calling upon to them to stop and engage with him. It's possible that they didn't see him (or hear him as the rider did have an earbud in), however, I think it's more likely they just didn't think they needed to stop (when I was 18 I was capable of coming to dumb conclusions).
Yeah, the whole incident seems pretty stupid. I don't like the fact when the rider is asked by the cop if he stopped at the sign he responds "Yes" when it was quite clear he didn't even casually "roll it". However, charging him with felony fleeing seems to be a egregious overreach. Cop should have just told him, stop when I tell you to stop and issued him a citation, and unless Florida is like California (which doesn't distinguish fines between autos and bicycles) it isn't likely to have been a really expensive ticket. Even though I think waaaaay too many stop signs are pretty bogus, you simply can't act the way this kid did.