Because your handwritten notes are "digital ink" they will stay the hard-coded color that you wrote them. "Marks on a page" (which is how M$ describes handwriting) is considered to be a kind of drawing, which has a fixed, hard-coded color, as it is NOT a font.
You can convert them using the built-in handwriting recognition to font(ed)
text (see bottom of this post) in which case you can apply "automatic" coloring, but then your handwritten notes are stuck as font text. If you are sure that you want to keep your handwritten notes as handwriting, the best you can do is to change their color to another hard coded color.
(Prior to Onenote 2010, all ink was considered drawings unless you were using an actual "tablet" PC)
In regard to changing the color of your handwriting in Onenote 2010, this is not a terribly difficult thing to do, but must be done separately on each page. For your reference, Onenote treats "Digital Ink" differently depending on whether it is considered Handwriting or Drawings.
In Onenote, you CAN change the color of
TEXT (fonts) and DRAWINGS, but you CANNOT change the color of "Handwriting" without converting it to TEXT or Drawing first. You can of course convert Drawings back to Handwriting after....
Please take a look at the example below:
It looks like a hand written note, and it was done with the pen (With a quick color change), but due to the way that onenote recognizes text, anything that isn't immediately recognizable as Handwriting is treated as a Drawing:
As you can see above, click-drag selecting the area shows 2 different selection types; a dotted box with handles for the drawing, and a standard onenote text box for the "Handwriting" ink. Interestingly, Onenote thinks that the "S" is actually a drawing!
Onenote treats "Handwriting" ink as text, but unless you convert the "Handwriting" to text or a Drawing, you cannot change the color.
To keep your handwritten notes intact, select all of the ink on the page (CTRL+A) or click and drag to select some of the ink, and choose "Treat selected ink as --> Drawing"
Now you can see that the entier area is treated as a drawing:
And you are free to select individual strokes of the drawing, and change their color with the color and thickness tool on the Drawing toolbar:
and then convert it back to Handwriting with a right-click:
Voila! You handwritten text has changed color and it is once again recognizable and searchable as text in onenote:
Please be aware that you can convert your Handwriting to
Text (with a right-click), and then change the color with the font color tool on the Home tab, but you can never change it back to your original handwriting:
...as you can see the handwriting is now text and the font tool can change the color!