Taken at face value, looking at the 40 odd shots Bayern had last night, the offside goal, the penalty, you could make a case for them being deserving of the win (I certainly wouldn't say you were unequivocally wrong because of it).
But 20 of those shots were blocked by Chelsea players. The penalty was saved by the Chelsea goalkeeper. The offside goal came about because Cole held his position and didn't stray behind Ribery. They restricted Bayern to an awful lot of pointless shots from outside the area and when they did break through, they were met by a great keeper. On the odd foray forward by Drogba Bayern's defence looked unsettled, and Chelsea took their chance.
Based on the penalty shoot out, Chelsea deserved to win because they put their shots in the back of the net. Based on the match itself, Chelsea deserved to win because they assessed Bayern's superiority in fluid passing football, looked to restrict it, and take their chances on the counter.
It's a bit of a shame I suppose that all that money has been spent on a team that has surrendered possession, but it doesn't make them any more deserving of winning because they did the job they were supposed to do. No one would argue Chelsea haven't been a travesty in the league this year, because over 38 games your squad can be accurately judged on its strengths and weaknesses. Chelsea are the sixth best team in England, which certainly doesn't make them the best team in Europe. But they are the most deserving of this trophy, for fighting tooth and nail, defending with their lives, taking their chances and countering a team's game plan.
Bayern's inability to win this rests on them. For that they don't deserve it, because they didn't address their shortcomings, they just let Robben cut in time and time again. Heynckes didn't really have a plan when faced with Chelsea, same as Barcelona didn't. So they stopped two of Europe's strongest teams, it isn't a coincidence.