As you must have noticed, using the Views integration of the Charts module, you can only select 1 color for each chart.
However, if you would rework your chart to a Combination chart, you could set a color for each of the charts. Here are some more details about how I'd create the combination chart (with 1 color for each taxonomy term):
- Use your current chart display as the parent chart for 3 child charts to be added to it (as explained below). Adapt its chart settings where needed, so that it won't get in the way of the 3 child charts to be added to it. for that, I'd make it a "line chart", possibly with some other refinements like color and label of that chart also.
- Add a 1st (child) chart display with a views filter that limits the values to only your 1st taxonomy term, and specify a 1st color in its chart settings. Use the first chart as its parent chart.
- Add a 2nd (child) chart display with a views filter that limits the values to only your 2nd taxonomy term, and specify a 2nd color in its chart settings. Use the first chart as its parent chart.
- Add a 3rd (child) chart display with a views filter that limits the values to only your 3rd taxonomy term, and specify a 3rd color in its chart settings. Use the first chart as its parent chart also.