1. Steam isn't taking away from your brand. Just put a logo screen in your game and other stuff to let people know you actually exist. There, you have your brand back.
This isn't really true. There's a huge difference between clicking through someone's logo at the start of the game, and being an actual fan who went to the dev's website (probably read the news/blog there) and purchased the game directly. The former is unlikely to buy your next game on brand recognition alone, the later will most likely do it. I know that I don't remember who made most of my Steam games, except the big ones that I've heard about before. I just got them because they were in a sale and looked nice.
There's a huge value in building a direct fan base. Especially with indie games -- supporting your favorite developers is a big factor here.
As for Steam's dominance (I've heard it stands for around 90% PC downloads these days, not counting casual games) -- one bad outcome are all those people who refuse to buy your game unless it's on Steam. It's annoying. But then again, it's hard to tell if it really affects sales in the big picture. It might be that thanks to Steam the audience of potential indie game buyers is bigger to begin with.