Fluxbox, like Blackbox, just has two wrapper utilities for this - In fact, they have the same names the as they do in Blackbox: bsetroot and bsetbg. Let's see how they work.
bsetroot is about the equivalent of xsetroot. It can set backgrounds as long as they're simple, like a solid color. bsetroot can also set gradients.
bsetbg is a higher-level program, sort of. It's actually a wrapper to other utilities that can set backgrounds, such as wmsetbg, Esetroot, the display program from ImageMagick, etc. When it's first run, it will create a ~/.fluxbox/bsetbg config file, which will set up which programs it can use. You can edit this at any time to select which to use. In order to use 'transparent' applications, such as xchat and Eterm with transparency, you should use either wmsetbg or Esetroot.
One of the shortcomings that Blackbox has is that the background is totally dependent on the theme. Whenever you change your theme, you have whatever background the theme author thought was right. A lot of people don't like this behavior. Well, Fluxbox has a way to fix that. Add a line like this to your ~/.fluxbox/init file:
session.screen0.rootCommand: bsetbg -f ~/backgrounds/zimdib_dark.png
And whatever you have put there, will be your background, no matter what your theme's author has to say about it.