you must find a way to be less worried about your critical comfort. there are some threads on here about what other gents have done to keep the "boys" safe and sound. do a search with something like "riding comfortable for men" .
But, there are clothing options that help with that.
you will get better at the trot and find yourself bumping less. it takes time to feel the rythm. I might suggest one or two private lessons to help you get the hang of it, so you won't beat yourslef to a pulp trying to get it.
The trick is to come down softly. the horse throws you up, you control the decent, and like you said, it's like standing on the floor, crouched, bobbing up and down. the energy comes in where you stop yourself from going further down and change downward energy to upward thrust. and also, like you said, it isnt' straight up, but rather in a kind of arc forward, with your pelvis front leading.