You don't have to be fancy to get your point across, but there's a reason graphic designers stay in business; beautifully presented information is more likely to be looked at, understood and enjoyed.
Take a look at these two flowcharts from the New York Times and you'll see what I mean. Click through to the Times to see them in their full glory.
The first, by Paula Scher, tracks how reactions to blog posts transition from amazement to antipathy to ennui. It's black & white, but the way Ms. Scher visually shapes her presentation adds mystery and meaning to what would otherwise be dull.
The second, by Sam Potts, honors the passing of Dungeons & Dragons creator Gary Gygax with a flow chart about the evolution of geekdom. Has he organized the information in the most logical way? No. He presents ideas in a maze reminiscent of the subterranean arenas Gygax envisioned. It's about geeks and looks like it.
When you're creating your own flowcharts, think of these excellent examples. It's not just what you're saying -- it's how you say it.