Contraceptives and their use is not a confusing issue for faithful Catholics. Since the Lambeth Conference of 1930, the Catholic Church has practically been the only major faith that still bans the use of contraceptives as sinful while the rest have allowed its use. She recognized that Truth cannot be changed, nor compromised, for then it could not be the Truth.
The use of contraceptives has been clouded by emotional arguments and a false compassion for couples who struggle with having children, and as a result, the faithful, including many Catholics, have fallen by the wayside and despite the Church's teaching against its use, have justified their using contraceptives in their own lives. Some have argued that the Catholic Church doesn't understand the plight of couples and having children yet it is precisely because the Church does understand that she issued Humanea Vitae. It was not just the plight of couples that she understood, but also the plight of all mankind. For faithful Catholics, there is no question its use is sinful, for that is what the Church taught. We may not have understood all the nuances in this teaching, but that was not the point. The point was that contraceptives were and are wrong and their use to prevent the conception of a child was sinful as taught by the Church. No moral confusion.
There is also no moral confusion to what the Church teaches about abortions. Abortion is sinful, period. There are no circumstances where it may be permissible, nor any justifiable reasoning where its use may be wrong but is needed to bring about a greater good. It is never lawful to commit a sin in order to bring about greater good. No confusion. Abortion is a grave mortal sin. Again, we may not completely understand all there is to know about why abortion is a grave sin, or even how to defend the Church's teaching against its use, but, the point is however, that what we understand or don't understand is not what matters, but to believe, trust and have faith in our Church's teachings, which are Christ's teachings.
People seem to have this desire to understand what they are taught rather than just accept a teaching without question. I too have this desire, but as in the case of John 6:60-63, 65-68, understanding is not always what it's cracked up to be. In John, Christ just finished telling his disciples that his body and blood is real food and unles they eat his body and blood they have no life in them. This was their reaction:
60 On hearing it, many of his disciples said, “This is a hard teaching. Who can accept it?”
61 Aware that his disciples were grumbling about this, Jesus said to them, “Does this offend you? 62 Then what if you see the Son of Man ascend to where he was before! 63 65 He went on to say, “This is why I told you that no one can come to me unless the Father has enabled them.” -
66 From this time many of his disciples turned back and no longer followed him.
67 “You do not want to leave too, do you?” Jesus asked the Twelve.
68 Simon Peter answered him, “Lord, to whom shall we go? You have the words of eternal life. 69 We have come to believe and to know that you are the Holy One of God.”
The disciples of course, did not understand how Jesus could say such a thing or even ask them to accept this teaching. Some of them left Jesus, never to come back. He didn't explain anything to them. He didn't expect anything from them except this: For them to believe His words, have faith in them and to Trust Him. Understanding would come later. Many failed to believe and have faith in Christ's words, just as they fail to do today when He speaks to us through His Church.
As far as the Real Presence of the Eucharist, again there is no moral confusion. The Church has always taught us that Christ is truly present in the Eucharist. Transubstantiation? I can give you a good idea of what it means, but never in its entirety, but that doesn't matter. The faith and trust I have in the Catholic Church to teach the Truth is what is required of me. That does not mean I have blind faith. On the contrary, I am at liberty and have the responsibility to pray for understanding. Understanding is not my first requirement, but rather, it is belief and faith in the Church's teaching. Once I accept this, then understanding comes later.
Catholics have been led to believe over the years that the morality of abortion and contraceptives are subjective, and that we have to work things out on our own as to whether or not they are sinful in our lives. This is NOT what the Church teaches and until Catholics realize this, then yes, moral confusion will reign in their minds. As faithful Catholics, we have it pretty easy when it comes to discerning whether abortion and contraceptives are sinful or not or the many other moral issues facing the world. The Church has taught consistently for two thousand years without change, and there is nothing confusing about them. The Church is here to teach and to guide us in faith and morals, if only we would believe, have faith and trust in her words.
What would Christ say if we told him we didn't know what to believe when the time comes for us to face him? I would imagine him saying, "Yes, you did know. I told you myself."