Portland is fantastic, and I'm surprised it didn't hit the list -- Rogue and Widmer in the same city? That's just unfair. That said:
Colorado is a pretty solid beer state, so while I'm generally unfamiliar with Denver, it didn't surprise me to see that hit the list. Proximity to Boulder and Fort Collins give it access to a number of really great breweries, e.g., New Belgium.
LA surprised me, though SoCal has solid breweries as well, and I can see picking LA over San Diego on sheer size, since I'm sure you can get the same beer in the two cities. If you have to have a SoCal city, which I find it hard to argue with, I think this is fine.
Cleveland is a sleeper. There are a lot of brewpubs and a few decent breweries in the metro area (way more than it seems), and seriously, if you live in Cleveland, you probably drink a lot. And with all of the fantastic Polish food in the area, it's definitely a town of beer drinkers. Great Lakes, for a relatively locally distributed company, has so many good brews. My favorite thing about Cleveland airport is that you can always find Great Lakes on tap.
http://beermapping.com/maps/citymaps.php?m=cleveland#
Philly, too, is a far better beer city than it seems. But top 5 is questionable. Yards, Flying Fish (NJ), Philadelphia Brewing, and Victory are the top breweries imo, and there are a number of brewpubs, but this isn't quite top 5 material for me.
I don't know SF well enough to judge, but I know there are a bunch of good NorCal breweries as well, so this isn't surprising.
Montana has some really nice breweries and brewpubs, but there are no cities, so that can't really make the list.
Bottom line: Philly out, Portland in. But if you don't include Philly, you'll get accused of being too west coast centric. So, I get it. But it's wrong.