To be pedantic, Protovis did also use SVG; it just had a layer of abstraction that somewhat obscured this, whereas D3's lower-level syntax makes it feel like you're manipulating SVG directly (making it a bit more intuitive to learn if you're already familiar with SVG).

I'll +1 the recommendation though. D3 is (unsurprisingly, coming from Mike Bostock: http://bost.ocks.org/mike/) brilliant.

http://mbostock.github.com/d3/