FusionCharts is a configurable JS charting library. You choose your chart, define the parameters (highly configurable, though) and then render it. FusionCharts' strength is ease of use, backward compatibility, theming etc.

Muze is data-first. You start with data, apply any operations (if needed), then render. Muze automatically detects the right chart for that and then renders. Also Muze allows you to compose any kind of cartesian visualization, as it follows grammar of graphics.

So if I've to explain this in a spectrum, it goes like this:

d3 (very powerful, high learning curve, you can do anything) Muze (data-first, Grammar of graphics oriented, compose viz) FusionCharts (chart-first, lot of depth in configurations, but can't extend yourself for new chart types)

Hope this helps.