Florian Meyer isn't a bad ref. He does all the right things, stands in the right place, listens to his assistants (who didn't make mistakes), but soon after the start of the match it must have dawned on the Czechs that he was easily fooled, and that was the way for them to win this match.
The Czechs turned out to be great divers, not like in the Italian school of diving - played with a lot of gestures and an angry face - but more artistic: just a quick nice roll and a look at the supposedly hurt bit of leg. It worked every time, even when the dive was a few seconds after the push. Florian Meyer fell for it all.
Ajax' Latin forward Suares was the only one from his team who understood what he had to do: dive in the box. And he did and Ajax had their penalty (which Huntelaar missed).
Later on when a Czech player acted out a very long fall which he managed to prolong all the way into the box, Slavia got their penalty as well. If you give both teams a penalty they don't deserve, your mistakes even out.
Apparently this is the 6th time Slavia try to get to the Champions League. This time they might succeed, Ajax lacks creativity and the Czechs are much smarter.