The correct answer is D.
A. “Why was my proposal not agreed to?” is a passive voice sentence. It is not clear who did not agree to the proposal.
B. “Why was my proposal not agreed by you?” is also a passive voice sentence. It is not clear who did not agree to the proposal.
C. “Why my proposal was not agreed to by you?” is a complex sentence with a subordinate clause. The subordinate clause is “why my proposal was not agreed to.” The main clause is “you.” The subordinate clause is not necessary to the meaning of the sentence, so it can be removed. The sentence becomes “Why did you not agree to my proposal?”
D. “Why did you not agree to my proposal?” is a direct question. It is clear who did not agree to the proposal, and it is clear what the proposal was.
The other options are not as clear or direct as D.