This is actually exactly what I thought as well. I think Thom accused Nelson of trying to seduce Milo, to which Milo said nothing, basically "confirming" it for his father.
Beautifully written chapter, but I will probably never read it again partly because it hit so close to home. From about 15 to 16, I was with someone so much like Milo (he was amazing when we were alone, casual acquaintances at school). The shit hit the fan when I came out, and he basically pretended I didn't exist from that moment on. Which is when I became friends, and eventually boyfriends, with basically my Brandon (on the football team and everything lol). Maybe that's why I'm rooting for NBITE so much?
Oy, this chapter really did knock me over.