It may not seem like it, but Roy and Armstrong share a very special bond. First of all, the Major was dispatched as a human weapon to the Ishval War, just as Roy was. He's called the Strong Arm Alchemist, but it's only ironic to see just what a soft and kind-hearted man Armstrong really is. His extreme kindness is the ultimate responsible for his retirement from Ishval, as his mind couldn't bear to see that much suffering and the fact that he was responsible for a good deal of it.
At that time, Hughes told Roy that was probably the best way to escape from that war -- but I don't think Roy likes to take the easiest path for anything. After the war, Armstrong was stationed at Central City and worked under Hughes. We don't know if Roy was an usual conversation topic between the two, but the truth is Armstrong's faith in Roy is absolute, whether it had anything to do with Hughes or not.
Hughes' death was a actually a hard blow for Armstrong too, and it's almost certain he's one of the few people who better understand Roy's feelings in that respect. Unfortunately for both Roy and Armstrong, the latest not being under direct command of Roy makes collaboration harder between the two. It's probably because of that, that these two normally engage in double-meaning conversations in order to keep the information flowing. Something beautiful to observe, if you ask me.
Armstrong: After experiencing that civil war, perhaps this country is coming to a point where it must change. And the one who can do that is a person who has known the pain of the battlefield and yet can calmly aim for the top, Colonel Mustang.
Roy: Now what are you talking about?
I love seeing people confide their hopes for the future on Roy, and Armstrong is definitively a good example of that. Despite normally hiding his most truthful opinions behind words, he's openly stated his trust in Roy -- his belief in entrusting Roy with the fate of the country.
No wonder it was him the one most affected when the Maria Ross incident took place. Armstrong just couldn't believe that Roy, the man he so fervently believed in, could have perpetrated such a cold-blooded murder, even if it was an act of revenge's for Hughes' death. I have no doubt that, had it been any other man, Armstrong would have punched him right there at that moment.
But those doubtful feelings don't last long, as Roy soon reveals the whole charade to Armstrong, mostly because he couldn't bear seeing the man in that state. Roy's excesive softness arises in key moments, much to his disadvantage, but also as a reward to those who follow him earnestly. In return, Roy does show a soft spot for Armstrong (as previously noted) and regards him as a man he can absolutely trust in -- which, out of his close circle of subordinates, is saying something.