I had the Minutemen attack the synths at Greygarden and failed the quest "underground undercover." Does this mean I can't finish the railroad quest line?

Yes.

Why did the MM attack synths at greygarden? I didn't do all the BoS or Institute quests but I didn't think there was more than the radiant quests and end quest for the MM unless it was a random encounter and you shot a flare. I'd think you broke the railroad quest line though if you failed the mission. You can go talk to the RR or do they shoot you on sight now?

They don't shoot me, but won't give me the next quest, it just says that "this individual is busy"