I believe it is mostly due to the laws of each state. Brewers Assoc. stats.
After prohibition ended, it was up to the states and counties to determine their own stance toward alcohol. One part of the repeal of the 18th Amendment was the legalization of homebrewing wine and mead. The law did not allow the homebrewing of beer until 1978. Event then, it was up to each state to determine their stance toward the homebrewing of beer.
The states with the most breweries per capita follow the federal statute, which allows for 100 gallons per person of drinking age up to a maximum of 200 gallons per year. The states on the map with the least breweries have only recently relaxed their laws on homebrewing and alcohol sales in general.
Many homebrewers dream of starting their own brewery or pub, but they need to be able to practice their craft. I am unable to locate the minutes to the Alabama House of Rep. discussion online, but the Basic Brewing Radio Podcast did air a snipped of the floor arguments on the legalization of homebrewing. Some of the arguments against were uniformed and antiquated.
Why open up a beer business in a city/county/state where regulations and attitudes are opposed to your product?