Certainly, I think lot of it is to do with the designers graphical abilities, or at least the time it takes to produce them. Most indie devs are one or two people with little to no budget, and are unwilling or incapable of creating huge amounts of hi-res artwork for a game. The smaller you make your graphics, the faster you can produce them. Certainly, for some of my projects I've used incredibly tiny screen resolutions in order to build much bigger worlds, with very low-res graphics. Look at Nifflas' games; they're about as small as they can get whilst still being visable, and yet he's used this to create intricate and absorbing worlds and an engaging art style.
Another problem, certainly in my case, is familiarity. You know where you stand with traditional low-res sprites: 16 x 16 blocks making up rooms, and the user simply scales the game up to their monitor size and it's all fine. With a high-res game though, you lose these restrictions, and then where do you start? Do you make the game at its maximum resolution, then somehow scale it down to fit smaller monitors? Or do you design it to fit the average monitor (1024 x 768 is, I think, still the most widely used resolution) and scale it up, risking the graphics looking blurry on high-res displays. How do you go about making it scale anyway? It's certainly something I'd like to look into. I'd like to do a high-res game, with lovely high-def artwork 'n all, but I wouldn't really know where to start. It is certainly a large technical barrier that may persuade the majority to stick with what they know, low-res retro graphics.