There are a number of factors involved. Primarily, I think, they boil down to economics (read MONEY!) which influences the probabilities for each team. Certainly, teams like Boston and NYY have solid baseball people but Money has bought them out of how many bad contracts? Could any team eat the contracts on Clement, Gagne (albeit half a season or less), Lugo, and Hinske (amounting to approx 26mil in salary) even though they didn't contribute much or play regularly (besides Lugo, and I tend to think they won in spite of Lugo, and not because of him). And NYY, with Pavano, Farnsworth, Mussina, Damon, and Giambi (ignoring the fact they paid 16mil for Pettitte, who's good but damn that's alot of cash for a 2/3 starter). Those players and their contracts would kill any other team in the league. When 3 of the 4 AL teams in playoffs occupy 1, 2, and 4 of the top spending teams in the league, it's hard to exclude economics as a factor.
However, on the flip side, the NL teams - Philly is sitting around 90mil, Milwaukee at 70mil, and both Arizona and Colorado in the mid-low 50's - are all mid-market teams. The only mid-market team to make the playoffs in the AL is Cleveland.
In addition, you have teams employing totally different strategies. The "experts" can rave about Boston and NYY developing their own players. They still can afford to out-spend to keep their own talented players and out-bid other teams from keeping the players they develop. Meanwhile, you have teams that developed the majority of the players in their lineup who are short of their Free Agency requirements.
There is an obvious factor that some teams simply cannot develop their own talent or are not very good at developing certain positions, i.e. positional players versus pitching. Houston would be, IMO, a fine example of a team that turns out servicable pitchers, with the occassional top tier pitcher, but struggles to turn out equivalent positional players. Philly, on the other hand, couldn't find a pitcher if he bit them on the ass, but sure seem to find positional All-Stars like they grow on trees (which I personally think is a factor behind Wade's hiring, perhaps meshing Houston's success with pitching and Wade's involvement in the success in Philly).
If anything can be taken out of this, I think that the next collective bargaining agreement will see even more revenue sharing. I'd also like to see a true slotting system for the amateur draft. It's bad enough that the big money teams have made the majors unduly influenced by economics. When teams have to avoid drafting amateurs because of the "Boras Factor", then the game is headed for trouble, again IMO.
Other than that, playoff baseball is all about streaks and riding the hot hand. If Colorado's pitching had held up against the Boston offense, and their hitters not gone ice-cold at the plate, this may not have been such a lopsided sweep. It's a crap-shoot... and a large part of why it's fun to watch the playoffs.
eta: 2007 Salary totals
http://asp.usatoday.com/sports/baseball/salaries/totalpayroll.aspx?year=2007