A big deal breaker is, of course, authority. The leaders of the early, yet unsplit, church, under the direction of the Holy Spirit, determined which books which would become the authoritative canon of Scripture. All Christians agree with that.
But the significance of making that determination was understood differently by those who became Roman Catholic/Orthodox and those who would eventually become Protestants. If I understand the Roman/Orthodox view correctly, the fact that the church leaders (Magisterium) decided what books constitute the canon shows that they--and the tradition proceeding from this and their other decisions--are of equal authority with the Scriptures and in a practical sense, even greater authority because the Holy Spirit gives right understanding of those books to them alone. The interpretation of the Magisterium trumps any other interpretation a reader of the Scriptures believes is from the Holy Spirit.
Protestants believe that the fact the church leaders decided what books constitute the canon shows that the Holy Spirit only enabled them to recognize those books which were inspired ("God-breathed") and that by so doing they were acknowledging the authority of the Scriptures over them, that all other authorities are subordinate to, and are to be corrected by, the written word of God.. Leaders and laypeople alike have no authority in themselves to "rightly divide" (interpret) the Scriptures, but, conversely, they have equal access to the Holy Spirit for the true interpretation.
This was one of "five solas" which led to the Protestant Reformation:
- 1 Sola scriptura ("by Scripture alone")
- 2 Sola fide ("by faith alone")
- 3 Sola gratia ("by grace alone")
- 4 Solus Christus or Solo Christo ("Christ alone" or "through Christ alone")
- 5 Soli Deo gloria ("glory to God alone")
Rather than focusing on his message, the Church responded by excommunicating the messenger.