Salomon Rondon's header at the death, canceling out Joe Allen's 73rd-minute finish, denied the Potters what would have been their first Premier League win of the season.
"I thought we'd done more than enough to merit three points to be honest," Hughes said.
"But that's sport. You do the right things for the most part and then you can still lose.
"That is how it feels at the moment. We have to remind ourselves it is actually a well-earned draw.
"Premier League points are hard to attain and we've been able to acquire one, so we have to take that from the game - but, clearly, at the moment it's a little bit raw.
"We think we certainly deserved the three points. It wasn't to be, but I was pleased with the performance.
"We are where we are the moment. We're off bottom, so that's a positive. We'll keep on building.
"It was seven games before we got a league win on the board (last season). We have Manchester United away next week, so we'll have to do it then."
For West Brom's ex-Stoke boss Tony Pulis - the predecessor at the Staffordshire outfit to Hughes - this was a 1,000th game as a manager.
Pulis received a warm reception from all sides of the Bet365 Stadium as he emerged from the tunnel just before kick-off.
And he said after the match: "You couldn't have picked a better place for me to get to 1,000 games.
"The place is wonderful. The crowd were absolutely fantastic to me as a manager here.
"It has been stitched into my body, this football club, in lots of respects. It is always a result I look for, and the Coates family (who own the club) are wonderful people and I'll always have respect for them."