You can target canvas with d3, but you loose much of the abstraction that makes d3 powerful. For example, look at all of the low-level canvas rendering code that is used. Not as powerful as visualizations driven by chaining .data().enter().append().attr() which can easily be re-shaped by swapping html tags and CSS attributes.

d3 really is a three-legged stool of HTML, JS and CSS. When targeting <canvas>, you loose both HTML and CSS and thus much of the power.

EDIT: I should clarify that I'm thinking of HTML in an abstract sense that also includes SVG. By hooking into the DOM, d3 gets a free scenegraph that makes it easy to modify the components of the visualization without writing low-level code.