Weather Spoons has the lobbying and buying power to buy thousands of barrels from suppliers, in advance, at a huge discount, and spread them across their many venues. They in turn can afford to make a loss on certain drinks and meals, as it's subsidised by other, more expensive drinks and meals.
Small independent venues buy a small number of barrels each week for one venue, and pay a huge amount more for them. Most are barely breaking even on drink costs.