He had at least 95 at odds with the Catholic Church.
You'll note that no where in the 95 Theses did Luther take issue with the Catholic Church. Thinking that the 95 Theses are "against the Catholic Church" fundamentally misunderstands the character and context of the 95 Theses.
Firstly, let's be clear what the 95 Theses were. Luther was the head of the theology department at Wittenberg University, and the church door at Wittenberg was the university's bulletin board. When faculty wished to debate a subject, they would post the topic of discussion on the church door.
The 95 Theses were written in Latin, they were intended as an invitation for discussion and debate on the topic of indulgences. Luther's intent was to defend Catholicism--and the papacy itself--against the abuses of the selling of indulgences. That was the intent and point of the writing and posting of the 95 Theses
against the selling of indulgences.
The 95 Theses aren't even really all that "Lutheran", but it does represent a point in time of Luther's thinking, which would mature in time.
A far more important set of theses are the 28 Theses of the Heidelberg Disputation (1518), here Luther's theology shows itself in a more mature way, in particular as he communicates the dichotomy of Law and Gospel, on the false theologies of glory and the faithful and truthful Theology of the Cross. It is here, in the 28 Theses of the Heidelberg Disputation that we actually start to see something distinctively Lutheran emerge--not in a vacuum, not in isolation, and not against the Catholic Church; but as a Catholic faith specifically shaped by the strong emphasis on Christ and His cross.
That true Catholic Christian theology cannot be found in the metaphysical conjectures of Scholastic philosophy, but rather instead only and solely by the Divine Revelation of God Himself in Jesus Christ. The philosopher's God is a hidden and naked God (Deus Absconditus et Nudus), and at best can only get us to the ignorance St. Paul talks about in Romans chapter 1, that God's power is displayed in creation, but men worshiped the creature rather than the Creator. Acknowledging God's glory, power, righteousness, wisdom, virtue, etc doesn't mean anything, even the Pagans recognize divine glory and power displayed in creation, but it does not lead them to the worship of the true God. Which is why it is only God incarnated, revealed, and clothed in Jesus Christ (Deus Revelatus) that actually shows us the Father, and is therefore the "Way, truth, and the life, no one may come to the Father except by Me".
It is in Christ that we meet God. And it is only in Christ that we can say anything meaningful about God, namely His weakness, humility, suffering, and humanity.
Speaking of the invisible things of God doesn't make one "worthy or wise" says Luther. Rather, true theology acknowledges God visible in the suffering and cross of Jesus.
God is found not in invisible things which we are left to speculate endlessly about; rather God is found in the manifest, visible, tangible, external things: there is true flesh, blood, and bones of Jesus' body; He died on the cross, He rose from the dead, He bears the visible marks of His passion, He is bodily present in, with, and under the bread and wine of the Eucharist.
This is not "against the Catholic Church". This
is Catholic Christianity.
So simply put, it's not Lutherans who left the Catholic Church. We never left, we were and have always been, faithful, believing Catholic Christians. It's Rome that is out of alignment with the Catholic faith. It is Rome that needs to be restored to communion.
That does not mean that we deny that Rome is truly a Christian Church. Roman Catholics are our fellow Christians, plain and simple. All who have received Holy Baptism are members of Christ's holy and Mystical Body, all who have faith are believers in the one and same Christ and sharers of the one and same faith; and thus we have drank from the one and same Spirit as St. Paul says in 1 Corinthians 12. It just means that, in its visible structures, Roman Catholicism is not "The Catholic Church", but she is, in the Communion of the Saints, heir to the same Church Catholic which Christ established through His Apostles.
-CryptoLutheran