The Early church had three criteria for determining what books were to be included or excluded from the Canon of the New Testament.
First, the books must have apostolic authority-- that is, they must have been written either by the apostles themselves, who were eyewitnesses to what they wrote about, or by associates of the apostles.
Second, there was the criterion of conformity to what was called the "rule of faith." In other words, was the document congruent with the basic Christian tradition that the church recognized as normative.
Third, there was the criterion of whether a document had enjoyed continuous acceptance and usage by the church at large.
The gospel of Thomas is not included in the Canon of the New Testament for the following reasons.
The gospel of Thomas fails the test of Apostolic authority. None of the early church fathers from Clement to Irenaeus ever quoted from the gospel of Thomas. This indicates that they either did not know of it or that they rejected it as spurious. In either case, the early church fathers fail to support the gospel of Thomas' claim to have been written by the apostle. It was believed to by written around 140 A.D. There is no evidence to support its purported claim to be written by the Apostle Thomas himself.
The gospel of Thomas fails to conform to the rule of faith. It purports to contain 114 "secret sayings" of Jesus. Some of these are very similar to the sayings of Jesus recorded in the Four Gospels. For example the gospel of Thomas quotes Jesus as saying, "A city built on a high hill cannot be hidden." This reads the same as Matthew's Gospel except that high is added. But Thomas claims that Jesus said, "Split wood; I am there. Lift up a stone, and you will find me there." That concept is pantheistic. Thomas ends with the following saying that denies women salvation unless they are some how changed into being a man. "Let Mary go away from us, because women are not worthy of life." Jesus is quoted as saying, "Lo, I shall lead her in order to make her male, so that she too may become a living spirit, resembling you males. For every woman who makes herself male will enter into the kingdom of heaven."
The gospel of Thomas fails the test of continuous usage and acceptance. The lack of manuscript evidence plus the failure of the early church fathers to quote from it or recognize it shows that it was not used or accepted in the early Church. Only two manuscripts are known of this "gospel." Until 1945 only a single fifth-century copy translation in Coptic had been found. Then in 1945 a Greek manuscript of the Gospel of Thomas was found at Nag Hammadi in Egypt. This compares very poorly to the thousands of manuscripts that authenticate the Four Gospels.