Los Colchoneros headed into their final encounter in Group B of the Europa League with a two-point advantage over the second-placed Czechs, meaning a draw would have sufficed to ensure the Madrid outfit top spot.
However, a first-half goal from Vaclav Prochazka was enough to give Plzen all three points and has seen them finish in first place ahead of Atleti."We would wanted to finish first in the group. In the second half, we played like we wanted to top the group. Maybe, we merited a draw," Simeone told reporters in the post-match press conference.
"But, we did not make the most of our chances. We played a good game in the second half and my players did what I asked them to. In the end, however, we could not equal the tie even though I believe that it would have been fair."
After both finished first in their respective groups, Liverpool and Fenerbahce are now possible opponents for Atletico Madrid, but Simeone refused to be drawn into speculation as to who he would want his side to be paired against.
He added: "When we find out about our opponents, then we will evaluate the situation."