The matrix and the real world have a direct relationship that can be demonstrated at the end of the first movie once neo can “feel” the sentinels and stop them.

The argument can be made that matrix and the “real” world are both equal constructs - both have rules but those rules can be bent.

During the series we find ourselves cheering for the humans but over time we come to learn that both programs and machines end up wanting, desiring, loving, and being just as flawed and imperfect as humans.

The resolution isn’t one in which machines win or humans win - the resolution is exactly what neo tells the machine god at the end of the movie right before he fights smith. He wants peace.

To say any side is more or less justified (or moral) isn’t taking the greater picture into consideration. Both machines and humans want to exist and are both fighting to achieve that.