Ryan Lowe volleyed in the only goal of the game early on to lift the Dons to within two points of top spot and leave hapless Pools without a win in 21 games.
And Hughes was left full of admiration for the Dons' slick pass-and-move style as his wait for a first win continues.
He said: "You have to be honest, we got quite fortunate to keep them down to one goal.
"They hit the underside of the bar and Scotty Flinders was magnificent - he must have had about five or six great saves.
"I questioned their goal, I thought it was offside but I've just seen the replay and it was onside.
"I was big enough and man enough to go along to the referee's room and shake the linesman's hand and say sorry, because he got it spot-on.
"I'm sitting back analysing it and if I can make Hartlepool as good as MK Dons then I've done wonderful job at this club.
"I'll take that on board and just keep striving towards that.
"But right now it's horses for courses and we will have to mix things up - I have to win football matches to give us a fighting chance to stay in this league."