The Gospel of Thomas isn't in the Canon because it was never part of the books which could have made it. It was never part of what the Church received and read in the churches, which was the single most important criterion for canonicity.
Think of the Canon in part as a legal document, like a constitution (this analogy is far from perfect), sometimes amendments are brought before the government's legislative body which may pass and be included, others don't pass and are rejected; while others were never brought before any legislative body whatsoever.
The books that are in, passed the Church's "legislature" by standing the test of time through centuries of consent among Christians and churches all over the Christian world; other books did not make it, they were filtered slowly because they didn't receive that mutual consent among Christian Faithful. Then there were books that simply were never part of the process at all, they were never read in any of the churches, they were never part of the Church's liturgical reading, never part of the Church's hymn and prayer life, never part of the universal life of the Christian Church. The Gospel of Thomas is part of this last group.
While Thomas isn't overtly Gnostic, at least not like other Nag Hammadi texts, it is still quite Gnostic in content, or perhaps "Gnostic-lite". It was written too late to be of any serious value to the churches, it never had a wide enough readership within the churches to "stick". These are just a few reasons, but in the long run it simply wasn't ever in the running and thus was never part of the Christian canon of Holy Scripture.
If you find personal value in Thomas, then good on you, though I would caution that one be able to understand that the text, if not heretical, comes quite close in a number of cases and should be read appropriately.
I find a number of statements in Thomas to be quite fascinating and worthy of note; but I also recognize that many are clearly Gnostic in character and therefore have no part of Christian orthodoxy.
-CryptoLutheran