Well, I don't use fluxbox myself, never tried either, but I'm a blackbox addicted
There's a tool for blackbox called bbconf, or either this would work under flux or flux would have a similar one to help you out with menu editing and it's links.
Try to find where and how xterm is inicialized thru flux and add the following to where xterm is called:
xterm -fn 10x20
That would make the font's bigger in xterm. Try openning an xterm as you do, and type the line above and you will understand what I mean by that. It will open a new terminal with bigger fonts. There might be an .fluxbox config file somewhere at your home... try looking after that and edit xterm to xterm -fn 10x20.
Sorry if I've made a mess here... Perhaps some flux user will help you out better if you did not get the idea