Do you agree with madison that the great compromise was not a true compromise but a rejection of the principle of majority rule

yes

Explanation:

Madison seeing the great compromise as not been a true compromise but a rejection of the principle of majority rule is very much understood because the Great compromise seemed to favor the larger states by giving them representatives in congress and in turn more power is delegated to them in congress. this will therefore limit the voice/power of the states with lower representation in congress.

The smaller states representatives initially  rejected this great compromise because they believed that states were just an entity occupied by people and the states should have equal power since they are on equal standings in the constitution.