Over the last 10 years the Supporter Shield winning team in MLS each season has averaged a winning percentage of 73.33% in regular season games that do not end in a draw. I know the draws mess that percentage up, and MLS lacks identical schedules, but over a decade I think this is a fair way to measure how often the best team in MLS wins rather than loses. Similarly, this does not directly account for injuries, or late season acquisitions who vastly improve a team, but again, I think a 10-year record evens those things out.
Now, admittedly, I get confused sometimes (embarrassing for someone who plays with stats and odds as much as I do), but I believe that calculating the chance, as of the playoff outset, that a team who wins 73.33% of its games will win MLS Cup if it has to win 3 straight games is simply 0.7333.. * 0.7333.. * 0.7333. Someone let me know if I'm wrong. But if correct, that comes to 39.44%. It goes down very fast.
Now maybe you think the best teams should be able to "turn it on" for the playoffs. I'm not convinced of that, but even if true you have to account for that fact that the 73.33% winning rate in the regular season is compiled against easier competition overall, which makes winning in the playoffs objectively harder.
Maybe you think the SS does not prove the best team. FIne, but it's hard to argue that a hypothetically better team should be expected to win at a higher percentage rate than it did in fact win, which would makes its odds even lower.
Bottom line - the playoffs is a game of darts played by drunks in a bar.
On top of that, winning the Cup can be so damn fragile and often too much credit is given when it's won, or too much blame is given when it doesn't happen.
For example, the Portland Timbers won it in 2015. They had a Cup-run deserving team, finishing 3rd in the Western Conference and winning the playoff games they needed to, but let's also remember that they barely scraped past SKC in the first round of the playoffs, winning 7-6 on PKs. SKC would have won the PK shootout except for Saad Abdul-Salaam's double-post PK miss.
On top of that, they beat Columbus 2-1 in the final, that included an early goal on a very bad keeper gaffe from Steve Clark.
I say all of that not to discount Portland winning the Cup that year, but to demonstrate that there is some luck that happens that happens to be much more impactful.
On the flip side, what if Matarrita doesn't commit that egregious penalty against TFC in the playoffs? Now, I know he has a bit of a history of some bone-headed plays, but I think that could be thrown into the luck category a bit. That team was talented enough it could have made a run to the Final that year. But instead, it was TFC that did it.
Cup runs are fragile and while still the ultimate goal (I believe for the majority of fans, but do realize not everyone), should likely not receive the credit/blame that is given when it is achieved or failed.
ETA: I do think the college bball analogy is a great one, because this exact same thing happens there. Since I attended Marquette, our best-ever tournament run was to the Elite 8 in 2013. That year, as a 3-seed, we barely scraped past 14-seed Davidson, needing a furious comeback over the final minute where we hit three 3's and a layup at the buzzer, while Davidson (one of the best in NCAA at taking care of the ball and hitting free throws), turned it over twice and missed two FTs. How close that team went from 1st round tournament failure to having a great tournament run.