The Honduras international, entering the final year of his contract, did not feature in the Premier League after February 1.
That was partly due to the form of youngster James McCarthy after his return to fitness, but Martinez believes the 26-year-old Thomas will provide valuable competition in central midfield after benefiting from a summer break.
"It can be difficult to keep people happy who are not in the team, but what's important is that the player realises it's a team game and everyone is going to have good and bad moments,'' the Latics manager told the Wigan Evening Post.
"Hendry is a player who needs to be at 100% from a physical point of view to be able to do himself justice and play his usual high-intensity game.
"Although he started the season really well he paid the penalty for playing in the World Cup last summer and not having a proper rest.
"The Premier League can be a really cruel competition in that respect and the season was probably a bit too long for him.
"Hopefully he'll come back for pre-season raring to go and will be able to rediscover that intensity that we all associate with Hendry.
"If he can do that, he'll give us even greater competition for places in that midfield.''