The home side ran out 2-1 winners in an encounter which saw Fulham striker Bobby Zamora suffer a broken ankle in a challenge with Karl Henry.
Wolves were shown six yellow cards and one red - Christophe Berra was sent off in injury time for a second bookable offence - but Hughes denied they were too physical.
"Wolves were competitive as you'd expect. Mick McCarthy sets his teams up to compete for every ball," he said.
"The Premier League is competitive and I've had similar criticism in the past. Sometimes it's warranted and sometimes it isn't.
"Maybe today some of the fouls were made to break up our momentum and maybe at times were a little bit cynical. That's why the crowd was getting frustrated.
"I'd never criticise any team for trying to be competitive against us - that's part and parcel of the Premier League."
New signing Moussa Dembele hit both of Fulham's goals, the second coming from the injury-time free-kick won when Berra was sent off.
"Mousa was excellent again and is an exciting player. When he's in possession you expect something positive to happen," said Hughes.
"There aren't that many players in the Premier League who have that ability.
"At times it felt like things were going against us - losing Bobby and we had two stonewall penalties turned down.
"When those things conspire against you, you believe that you won't get what you deserve but we were rewarded in the end."
Fulham fans chanted "you're a disgrace to the Premiership" at Wolves in the second half and McCarthy insisted his side are earning a reputation they do not deserve.
"I think it's grossly unfair. I'm really sorry to hear about Bobby but Danny Murphy came to me and said he'd have a word with Bobby because it was a fair and good tackle," said McCarthy.
"We were involved in a tough game on TV a couple of weeks ago and suddenly we're the devil incarnate, but we're far from that. We compete and compete fairly.
"We had some silly bookings and I'm mad at Christophe for getting sent off.
"But I don't see us as some overly-physical team that deserves that sort of treatment."