Like Eric said, there may be some other point that he meant, such as it is OK to be human and have trouble grasping this miraculous Sacrament. But the fact that we can't fully understand it, doesn't mean we don't affirm what we know to be true according to the mysteries revealed to us by Christ in His Church. A good homily should always bring people back to what grounds us in truth, not leave us in confusion.
Too often the confusion that was imparted to priests in their formation trickles down to the flock, and so the lukewarm (being confused) give up.
If you get a chance, take the deacon aside and ask him what he meant; that may be helpful. He may not realize how he came across.
If he did mean the worst interpretation, set him straight, albeit gently. Preachers need to know people are listening and thinking critically as well. In these days of confusion, we must test everything (1 Thessalonians 5:21-22) and hold our teachers accountable.