Messi, who has excelled in so many past appearances in Europe's elite club competition, was strangely subdued during the 1-0 reverse at the Calderon, which sent Atletico through to the last four 2-1 on aggregate.
"It is so hard to be Leo Messi in this life and playing football," Martino, who comes from Messi's home town of Rosario in Argentina, said at a news conference previewing Saturday's La Liga match at Granada.
"Basically because everything is so unfair. When he doesn't play as well as people expect him to he ends up being criticised very strongly," he added. "I think it must be very hard to be him."
Barca will need Messi to make a swift return to top form if they are to rescue their season following Wednesday's failure to reach the Champions League semi-finals for what would have been a record-extending seventh consecutive edition.
They are a point behind La Liga leaders Atletico, who play at Getafe on Sunday, with six games left and play arch rivals Real Madrid in Wednesday's King's Cup final in Valencia.
Martino, in his first season in charge of a European club, said Barca's Champions League exit had been a painful experience and even winning La Liga and the Cup would not dispel the sense of failure.
"I will be happy if we win any other tournament but for me being the new one playing in Europe and the expectations I had for the Champions League this was a failure and will remain a failure no matter what happens," he told reporters.
"After what we went through a team cannot be on top emotionally speaking, but we understand there is no time for grieving. What happened happened and now we must focus on what comes next."
Martino will need to reshuffle his defence for the trip to Granada after Marc Bartra picked up an injury in training on Friday and joined fellow centre back Gerard Pique in the treatment room.
Alex Song or Sergio Busquets may be drafted in to play alongside Javier Mascherano, who is also a converted midfielder, as captain Carles Puyol has yet to make his return after injury.
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