Since it said that 40% of the retail cost is Federal, State, and Local taxes, I would assume that includes beer and non-beer related taxes, along with liquor licensing fees for the retailer, sales tax on final sale, business income taxes for everybody, etc.
Not to say that it isn't also 40% of the cost of producing beer. Taxes on beer production would be a percentage of total taxes, but costs of beer production is also a percentage of the retail price.