"I won't go to school because I have a headache."
Based on a bit of Googling, it seems that the following are true:
から indicates a reason based on a subjective judgment and is often found in sentences where the main clause expresses a desire, supposition, prohibition, order, or request.
ので indicates a reason based on an objective fact, and is more polite than から.
In most cases, the two are interchangeable.