The Latics scored three unanswered goals against the hosts Royals and had 70% of the possession over the course of the 90 minutes.
"We had so much of the ball and so many chances, our superiority means we deserved the three points. We were worthy winners. I have seen Reading play the last few games at home and they have been very impressive," he told BBC Sport.
The victory has moved Wigan out of the Premier League's relegation zone with 11 matches left to play.
However, Martinez has admitted that it will still be "difficult" for his side to retain their status as a top-flight club.
"The challenge is to stay in the Premier League," he said. "It's not an easy one.
"It's going to be difficult. There are 33 points to play for and I do feel it is going to go down to small margins."
Next up for Wigan is a home match against Liverpool a week today.