A late Jack Grealish goal rescued Aston Villa a 1-1 draw in the final game of the season at Villa Park and handed Newcastle United the title.
Albion had led 1-0 with just two minutes remaining owing to a Glenn Murray penalty before the equaliser sent the trophy to St James' Park.
The Seagulls had needed just three points from their final three games, but missed out with two defeats and one draw.
Hughton said the scenes of Albion players collapsed on the pitch at full-time showed what it meant to them, but pointed to the fact that promotion to the Premier League is the silver lining.
He admitted: "I think what it showed is what it meant to the players and probably because of the timing of the goal, we have all been involved in games like it.
"If Villa had scored earlier and we were pushing and pushing then we are trying to get back into the game, but at that stage of the game it made it even tougher for the players to take.
"We spoke after the game and what you have to do is speak about the season. Because we had three opportunities to do it, out of three this is our best performance. Our best opportunity was a home to Bristol City in our last game.
"What we desperately wanted was to make sure we put in a performance that was more like us and I think we got that. I think the responses of players afterwards showed what it meant to them and you want them to have that disappointment, you want them to feel that way, because that is when it really matters.
"It's about reminding them that it would have been the real total this season. We have managed to finish just slightly behind a Newcastle side that has spent massive in the summer and that our a Premier League outfit.
"We have also managed to finish a good few points above the team below us and we have done that for two years. Today is a negative day and it's difficult, but there are far more plusses. What these lads have achieved this year has been magnificent."