Let us say I listen to a piece of music and I find that it is not rhythmically complex. I want to express that idea using the word 'simple' as opposed to the word 'complex'. If I say it was not rhythmically complex, it might have negative connotations. My feeling is that in such a context I could use (b) and (c) but not (a). Is that correct?
a. The piece was simply rhythmic. -> the piece was absolutely/extremely [and delightfully] rhythmic. In BE at least, the word 'simply' is often used (usually higher register) as an intensifier in the sense of purely, perfectly, solely, etc.
C: "How was your evening at the concert?"
D: "Simply perfect - it could not have been better."
Your examples b and c do still have a small possibility of being seen as negative, and you will need an adjective to set that aside:
The rhythm had a pleasing (or suitable adjective) simplicity.
The rhythm had the advantage of simplicity.
or (using a negative)
The rhythm was uncomplicated/ unpretentious/ not overwrought, etc.