The west London side sit on top of the early Championship table after two goals in the first half from Aleksandar Mitrovic and Fabio Carvalho.
The hosts took the lead a minute after Tim Ream went off as Mitrovic flicked home a corner from Jean Michael Seri.
The second came two minutes after Kenny Tete limped off, as a low cross by the impressive Antonee Robinson from the left led to Carvalho’s strike.
Tigers’ boss McCann felt Fulham’s opening goal should not have counted as he claimed referee Tim Robinson missed a foul on Jacob Greaves by Mitrovic.
“Their first goal I’m really disappointed with,” said McCann. “Having watched it back it’s a block on Jacob. It’s disappointing because it’s right in front of the referee.
“Fulham are a possession-based team, we have to stay compact and in shape. I think we did that in the second half.
“I was proud of the boys after the break, particularly for the way we stuck at it.
“I thought we started the game very well, they came down from the Premier League last season.
“We showed bravery, I asked for that and we showed it in the first half. We got forward in some good areas.”
Managerial counterpart Marco Silva, meanwhile, believes the hosts were not at their best at Craven Cottage.
Despite a performance that saw them dominate throughout, despite Ream, Carvalho and Tete all being forced off through injury, the Portuguese head coach felt his side could have played even better against his former club.
He said: “I’m happy with the three points, because we asked our players before the game to aim for the target of the third win in a row, with the first home win as well.
“If you achieve that, then I’m happy.
“It wasn’t the best performance to be honest with you. In this competition, with the level that you are, it was not the perfect performance that we had against Millwall.
“We have to play to win football matches.
“Today, we won the game because we were the best team on the pitch.
“After our first goal we saw confidence and controlled the game better, in the way that we wanted.
“Antonee Robinson is in our model, in our way to play. It was his best performance this season.”
Fulham: Gazzaniga, Tete (Reid 32), Adarabioyo, Ream (Mawson 21), Robinson, Onomah, Seri, Kebano, Carvalho (Zambo 70), Cavaleiro, Mitrovic. Unused substitutes: Rodak,Bryan,Francois,Stansfield.
Hull City: Ingram, Coyle, Bernard, Greaves, Elder, M Smith, Smallwood (Eaves 77), Williams (Emmanuel 46), Docherty (Cannon 86), Lewis-Potter, Magennis. Unused substitutes: Baxter,McLoughlin,Huddlestone,Jarvis.
Referee: Tim Robinson (West Sussex).