With the discovery, in the 1950s, of the Nag Hammadi library, in Egypt, much has changed in the study of Gnosticism, and of Late Antiquity at large. Scholars have been able since then to examine and comment on actual texts, rather than relying on patristic sources, and offer a clearer picture of both pagan and Christian Gnosticism.
Among the discovered texts was a copy of the Gospel of Thomas, written in Coptic. Of later origin than the Greek fragments (Oxyrhynchus, dating circa AD 200), this Coptic version (written circa AD 350-400) is however a complete text.
Perhaps it is because of its inclusion in the Nag Hammadi corpus that the Gospel of Thomas has been associated with Gnosticism, thus with heterodoxy. But a close study of the text would show that the Gospel of Thomas is as Gnostic as the Gospel of John. It is esoteric and somewhat dualist but lacks the Gnostic mythology and theology of, for instance, the Hypostasis of the Archons.
Why did the fathers and the council which produced the biblical canon reject the Gospel of Thomas? A first obvious, albeit sophomoric, reason may be that the text was not known by the time of the formation of the Muratori canon (circa AD 180) hence its exclusion.
Another and more accepted reason is that the Gospel of Thomas belongs to a category of texts called "wisdom literature." It is a collection of sayings, uttered by Jesus and gathered up by Thomas and his school. It presents an image of Jesus, not as the messianic savior, not as the incarnated Word, not as the son of God, as the canonical gospels do, but as a teacher, a wise man, a spiritual master. As far as the Church is concerned, a gospel which doesn't reflect the kerygma isn't worthy of the title "gospel" and doesn't deserve to be included in the canon. This is certainly what happened to Thomas, let alone to the Gospel of Philip.
A third reason for the exclusion of Thomas from the canon--and it is a reason which follows from the one above--is the lack of passion narrative. Albeit inspired by the Holy Spirit in their decision making process, the fathers who developed the biblical canon had a clear agenda: to fight heresy and the heterodox teachings of certain Christian groups such as the Marcionites (followers of Marcion), the Docetists, the Gnostics, etc. The passion, crucifixion and resurrection of Jesus stood as the basic of the orthodox sense of Christian mythology. They ensured the reality of the life and death of the Son of God, at once real God and real man. The Gospel of Thomas lacking a passion narrative was not a strong enough source, a reliable enough witness to be included in the canon.
Do all these reasons for the exclusion of the Gospel of Thomas constitute a basis for heterodoxy? Not really. The litmus test for orthodoxy is whether or not the ideas expressed in a particular text reflect the general teachings of the Church. What are then the basic principles expounded in the Gospel of Thomas? We can divide the text into two main categories: the "source" sayings and the original Thomas sayings.
The "source" sayings or the Q parallels are those sayings which come from an unknown yet common source (or "Quelle" in German, hence the term "Q") borrowed by both Thomas and the Synoptic Gospels. Those sayings are wisdom sayings such as "Blessed are the poor for theirs is the kingdom" which developed into the Sermon on the mount/in the plain in the Synoptics.
The other category of the sayings in the Gospel of Thomas are unique to the text and they give it its esoteric overtones. The principle behind them is however one which is found in the canonical gospels: "the kingdom of God is within you." The teachings of Jesus are thus "gnostic" (gnosis being knowledge) in that they help the believers/listeners discover or know the true meaning of their existence, of their origins, and lead them back to that state, the state of illumination, which is of course God. At that level, the Gospel of Thomas resembles the Gospel of John. Both are mystical, esoteric gospels. But neither one is truly Gnostic.
Now that the Church at large has transcended its original concern with christological heresies, it is perhaps time for Christian ecclesiastical bodies to rehabilitate the Gospel of Thomas, to try of understand it in the context of recent biblical scholarship and to use it for teaching.