Why were some books of the Bible almost rejected by the early church?

There were several “church councils” that took place between the years 200-500 AD that were supposed to establish the canon of scripture that we call the New Testament.  However, many of the people on these councils were influenced by non-Christian philosophies and false doctrines that entered the “mainstream” church and argued about the authenticity of several books of the New Testament, including Hebrews, 2 Peter, and Revelation.  They tried to discredit the apostolic authorship of all 3 in an effort from keeping them out of the Bible.  The reasons for this is the fact that they referenced Israel as being restored and placed a very negative view on Rome.  However, even though these books were disputed by man, the Holy Spirit guided those who were truly saved, and they were added to the canon (they also had tradition of being accepted for many years by many sub-groups of Christians).  The Bible has been attacked since the beginning, but God has preserved His Word through it all (Psalm 12:6-7).