The left-back’s header from Paul Gallagher’s corner levelled things up 10 minutes into the second half.
But at 1-1 Alex Neil’s side could not kick on, the Lilywhites conceding poor goals as Tom Anderson and Mallik Wilks sent the visitors into round four with a 3-1 win, John Marquis having given Grant McCann’s men an early lead.
“I’m chuffed to get the goal to get us back into the game,” said Hughes.
“It was nice to finally meet one.
“By the time my one went in I think Gally’s already put 15 crosses on the money.
“We looked at them defending set-pieces in the week and we’d seen that it was a weakness of theirs.
“It would have been disappointing for one not to have gone in.
“But a 3-1 defeat at home is never a good result and I can’t be taking any credit myself.
“We knew what to expect before the game and knew it was going to be tough.
“I played under Grant McCann last year at Peterborough and know he likes to play expansive football and I thought they did that well.”
Hughes could have added to his tally further on the day, seeing one shot saved and another hit the post before his 55th-minute goal.
“I hit the half-volley well but it was straight at the keeper,” said the 26-year-old.
“If it had gone either side it might have given him a problem.
“I hit the post too so maybe it should have been a hat-trick with a bit of luck.”
Those were rare bright moments though in a game where PNE were well below-par, Marquis’ goal five minutes in setting the tone.
“The last thing we said before we went out on the pitch was that we needed to start well and get the crowd behind us,” Hughes said.
“For some reason we couldn’t do that.
“We were in the game though and at 1-1 it looked like we were the only team that was going to go on from there.
“We were the team dominating but they stood strong.
“At 1-1 at home with the crowd behind us I thought we were the only team going to win.
"It was such a blow to concede from another set-piece for the second goal.”