I don’t really know much about beer bottles, other than Sierra Nevada’s, which I seem to be becoming an expert on. 
I do know more than I ever expected to about wine bottles, however.
First, clear glass is called ‘flint’ in the industry. Brown is ‘amber.’ (Sorry, it was driving me crazy)
If the beer packaging industry is anything like the wine packaging, there are probably 5 or 6 different ambers. (Light Amber, Dark Amber, etc., who knows.)
To answer Case Sensitive’s question, some wine does come in amber bottles. OK, actually I can only think of one varietal, Gewurztraminer, but still.
Just from reading this thread and a few of the linked pages, I’m personally coming to my own conclusion, which is a mixture of the 2 main reasons given.
The UV light affecting the beer, and marketing.
I’m basing it on my knowledge of wine bottles. Like John F said, reds aren’t bottled in Flint, they’re bottled in different shades of green (Antique Green or Champagne Green usually, both fairly dark.) But whites are, like Sauv Blanc or Pinot Grigio in Flint or Chard in Dead Leaf Green (a light, almost yellow color.) (Pinot Noir and Syrah are usually in DLG as well.)
There are definitely chemical reasons why reds are in dark glass and whites are in light, and it was obviously discovered centuries ago. So, even though times may have changed, and we are able to preserve the product better through, I don’t know really, better transport and/or storage, whatever, or if the finished product never sits on a shelf long enough to be noticably altered by exposure to UV light, consumers expect to find that certain style of wine (and maybe beer?) in that certain style and color package.
I’ve noticed in this thread that examples of beer in flint or green tend to be lighter styles, lager/pilsner, etc., while the darker ales and stouts are in darker (amber) bottles. Perhaps the Germans/Czechs/etc. found the green glass preserved their product better, and found it more appealing than another color (like amber), or perhaps it wascheaper or more readily available then*, and so began the great green glass trend.
*If, for example, many of the large breweries started noticing the green glass=better tasting beer after transport, the longer runs at the glass house would be economical to the smaller breweries, since changing color for a smaller run would increase the cost.
The same reasons now, that you’ll generally find certain wine varietals in certain wine bottle shapes (and color, to a small degree) . Although this is certainly not a hard and fast rule, you’ll tend to find the varietals made famous by the Bordeaux region in France in Bordeaux (Claret) bottles - Cabernet Sauvignon, Sauvignon Blanc, Merlot, etc. And you’ll find those made popular in the Burgundy region in Burgundy bottles - Chardonnay, Pinot Noir, etc. Same for the Alsace region (Hock bottles), and Champagne.
Anyway, just my WAG. Time for me tro drain another amber bottle.