My 2 year old is taking amoxicillin right now for ear, can he still get epiglottis or would the amoxicillin prevent it cause its bacterial?

Unlikely: Epiglottitis usually presents abruptly as the presenting illness in a kid under 5. The introduction of the current HIB vaccine given in early infancy has reduced the frequency of this disease by over 95%. Amoxicillin and it's earlier cousin ampicillin easily kill this germ. Any kid who is up to date on his shots & on amoxicillin is unlikely to have epiglottis, ever.