Atletico eased into the UEFA Champions League last 16 thanks to Mario Mandzukic's hat-trick in Group A action at the Vicente Calderon.
There was no repeat of Olympiacos' shock 3-2 win on the opening matchday as the Greek champions were put to the sword by last season's runners-up in Madrid.
Olympiacos goalkeeper Roberto Jimenez - an Atletico youth-team graduate - gifted Raul Garcia a ninth-minute opener.
Mandzukic doubled the lead with a 38th-minute tap-in before the Croatia international striker completed the scoring with two quick-fire headers in the second half.
"I feel bad because tonight we couldn't compete like we did in previous matches," Michel told UEFA.com.
"It's not because we did some things wrong, it's because our opponents did many things well.
"We have to accept that. Even when we do things well we still might not win, as happened against Juventus."
Michel also refused to blame Jimenez, who was at fault for Atletico's opening goal of the match.
"I'm not going to single out one player and it would be unfair to pick out Roberto because he is giving us a lot but it's true that the first goal was the beginning of the end," said the 51-year-old.
"This result shows you how important what we have done so far in the competition has been."
Olympiacos (minus 5 goal difference) - three points adrift of second-placed Juventus (plus 3) - are all but consigned to Europa League football due to their inferior goal difference compared to the Italians heading into the final matchday.
Michel, though, is not disheartened by the chance of competing in Europe's second-tier club tournament, conceding Olympiacos are not on the same level as Atletico and Juve.
"Atletico and Juventus have done their jobs. Let's do our job thinking that the UEFA Europa League is not a bad competition for us," he added.
"There is a difference between some European teams and us.
"We are at a different level. Atletico and Juventus are going into the next round."
