Jarrett has been pushing the idea of frequent bus network maps for some time now. I think they're definitely worth trying. In his latest post, he invited transit planners to comment on the idea. One concern was that if you choose an arbitrary headway like twelve or fifteen minutes, in some systems you have almost nothing on the map, and in others it's still too crowded.
The thing to do, I think, is to keep in mind that you're just trying to present the most frequent routes, and "most frequent" is relative to your system. I would suggest just starting with the ten most frequent routes. If the map is still too crowded, then drop a few routes; if it's too sparse, add a few, until you get the right information density. Conduct a few interviews with your target demographic, or throw a draft at a focus group, to see if you've got it right.
A challenge I see, that I don't recall anyone else raising, is how to represent corridors where multiple less-frequent routes work together to provide frequent service, for example on Fifth Avenue in Manhattan. On corridors like this, you often find people who take advantage of the frequent service but do not use the less-frequent branches. This could be handled with line thickness, so that the frequent corridor is thicker than the branches. That's the best thing I could think of; I'd be interested to know if anyone else has a better idea.