The complexity and flexibility of D3.js results in it being a time-consuming tool to learn for many users.
D3 is incredibly flexible; probably more so than any other JavaScript visualization library at the time of this posting. With that flexibility comes increased complexity. If you just want to create some quick charts you will get results faster with something else.
Selections are core to working with D3 beyond the basics. They're powerful and useful, but require new developers to get up to speed (e.g. set aside 30m to read and digest: https://github.com/mbostock/d3/wiki/Selections) and if used in the context of a larger application will result in a portion of the code using different patterns than the rest, requiring a translation layer in between.
Chart.js currently offers only 6 graph types, and lacks the flexibility offered by other options. For example, controlling the display of tooltips is fairly limited.
For the free version officially supports: R, Python and Matlab. There is also a Julia library.
The paying hosted version supports many more (excel, Scala, F#,...).
Flot provides detailed and well organized documentation that includes plenty of code examples you're free to use. It's fast to customize and add functionality, partially due to its use of jQuery.
Declare the type of chart, the x and y variables, and other chart properties. No unnecessary manipulation of data objects into separate arrays for each axis.
d3fc provides a number of higher-order D3 components that make it easier to build charts. With d3fc you can create series, annotations, samplers and layouts using the familiar D3 data-join pattern.
If you're using AngularJS, then you're two steps away from having beautiful charts.
n3-charts is simple to set up and use, with plenty of examples to help get you started.
If you are just starting off with a JavaScript charting library you shouldn't invest your time learning jqPlot. Once a great tool it hasn't been updated in several years and there is virtually no activity on the Google Groups forum these days.