Andy Monkhouse struck both goals for Pools, who were denied a last-day win by a late equaliser from Jamie Proctor, who also fired a double.
Hughes stressed there was no quick-fix and that League Two would be a testing division to come out of.
He said: "I know what we're up against and I know there will be a lot of hard work done in the close season.
"You have to be invigorated and excited, but I'm encouraged as looking at this performance you wouldn't think that we we are a relegated team."
Hartlepool faced a massive task to stay up after a shocking start to the season, but Hughes felt his side should not have gone down.
He said: "I was hoping for a good start (after replacing predecessor Neal Cooper), but the confidence wasn't there.
"I've had a good response and the boys know I'm with them. Now I'm looking forward to next year."
Hughes had nothing but praise for the band of 417 travelling fans, 130 of whom dressed as penguins as an end-of-season fancy-dress tradition was maintained.
The Scotsman added: "I take my hat off to all of them. It was a great effort. It was all about the supporters. I'm just a little bit disappointed not to close with a victory."