I've ordered from: Dominion City, Sawdust City, and Blood Brothers. All did a good job.
I only have two issues ordering direct from breweries:
1. Delivery costs add ~buck-a-beer
(or more if you don't get a full case) ... to already premium priced (i.e. expensive craft) beer.
2. Stale beer.
From one brewery I received 6-month old blond ale, 4 month old brown ale, and 2 that seemed lifeless (no date on cans). Only 2 of the 6 different beers were relatively fresh.
I understand breweries can't afford to dump stale beer, but I think it hurts their reputation if they ship it. Leave the "stale" beer in the bottle shop and let walk-in customers decide if they want to buy it - with full knowledge of what they are getting.