I disagree with the idea that harmonic progression should arise as a mere byproduct of following the rules of counterpoint. Some of the worst, most aimless-sounding music I've ever written came about as a result of writing counterpoint without considering the resulting harmonies as entities in their own right. I would even go so far as to say harmonic progression is more important than counterpoint. Plenty of nice-sounding music has limited contrapuntal value, whereas very little music with poor harmony is going to sound appealing. This is because human beings mainly perceive wholes (in music, this is harmonies), with the parts within those wholes being of lesser prominence.