Beer bottles that are colored dark brown prevent sunlight (UV light) from chemically altering the taste of beer and making it smell skunky.
“Scientists discovered that Ultra Violet rays from the sun break down the alpha acids in hops which then react with the sulfur present in beer to form a chemical that is almost identical to the chemical that skunks use to spray predators. Those damn UV rays. The solution was to tint the beer bottle to protect it from UV rays. Similar to how sunglasses help protect your eyesight; the dark brown beer bottle helps protect the beer from going bad.”
Source: Berghoff Beer