Men are expected to shower in front of other men at the gym in most cases i think, this may be his way of making the experience natural for the boy.
Seriously, unless you are getting weird vibes, you really should see that this is just what good dads do, they get their kids clean however.
I assume "He" is your boyfriend and the child is not from you and you have not been around for all the child's life.
My husband takes a shower with our 9-year-old son and it's not nasty. They don't shower together all the time, but sometimes our son climbs in with him. He's still a little boy in many ways. There is nothing sexual about it. Sorry you are seeing it as nasty in "his" case.