I've tested the same basic example with the latest build of Prince. I don't see anything in the chart on the pdf document (or it's really really small), using Acrobat Reader 11. Note that the box containing the chart is there, it just doesn't show anything. The same pdf also crashes evince (2.30.3), with the following fatal error: "floating point exception" (a division by zero?). Did you apply any special tweak to the original flot example?
Our goal here is to reduce dependencies on other tools and simplify the workflow (currently, we go through wkhtmltox in order to produce bitmaps for charts, and then rewrite the html to refer to these bitmaps). We are not necessarily stuck with the 'flot' package, especially if you tell us that it won't be supported by Prince in the near future. Do you have a recommendation for another js charting package that would be better supported by Prince?
FWIW, we decided to follow another direction and produce directly SVG charts from our application. Prince works beautifully on them We now avoid the dependency on both flot and wkhtmltox, which is great.