The west Londoners were unable to eke out a winner against the Toffees as they failed to make the most of home advantage once more.
Bobby Zamora's bundled effort saw QPR come from behind to secure a 1-1 draw, but means the Hoops have secured just two victories from 14 league matches at Loftus Road.
Despite dropping two points, the manner of the performance left Hughes believing they can stay up.
"I saw more qualities I expect from teams that I am in charge of," the Welshman said. "It has taken a little while but I saw things that I was encouraged by.
"I saw things that obviously really illustrated the message I have been trying to get over.
"They have to keep following what we are saying and understand what we're talking about.
"I have been in this league a long time and I understand what it takes to win Premier League games.
"I sensed against Everton there was a real understanding of what is required and that is what we will have to have from now until the end of the season."
Next up for Hughes' side is a trip to fellow strugglers Bolton on Saturday.
The Rs can welcome back Samba Diakite and Djibril Cisse for the match, with the latter's return particularly important with QPR struggling for goals since Hughes' arrival.
"I am not worried about goals with the team that we've got," Hughes said. "The one thing we have is a threat.
"We have Djibril Cisse coming back next week so I have no doubts about us.
"I would be more concerned if I felt we didn't have the ability to score goals in the Premier League.
"I know we have that threat and we can get organised to make sure we are difficult to beat and definitely have enough going forward in the games that we have left."
While his team is not of concern, Hughes did admit the Loftus Road pitch is slightly problematic.
"The pitch isn't ideal. It isn't great," he said. "At times we're taking just a little bit more care possibly just because it has deteriorated a little bit.
"We're in early spring now and it is starting to grow and the surface from now until the end of the season will be better for us.
"Obviously we're a footballing team, we want to get it down and play, but it is just comprising us somewhat at the moment."
Everton counterpart David Moyes was equally unimpressed with the pitch, but was far more complimentary about on-loan Real Madrid midfielder Royston Drenthe.
The Dutchman put in a superb performance and broke the deadlock with a fizzing left-foot drive which flew in from 30 yards.
"It was a really good goal coming off the line and he has been good for us," Moyes said. "He scored a few goals for us and they have been important.
"The attacking side of his game is very good, it is just the other side of it that sometimes worries me.
"It has been a little bit easier to use him at home than away, but he is adapting. It has taken him a little while to do so but he is getting better.
"He is scoring goals and getting assists as well, which is really important."