The Gospel of Thomas ignores John the Baptist for the most part. He is mentioned in Logia 46 (+47?) and 78, but that's it. When juxtaposed with the Synoptic and/or Johannine Traditions the Baptist is a minor figure for this segment of the Jesus-Movement. I've batted around in my head a rational for this: Geographical differences, i.e., there was less of a Baptist-Community where Thomas was written than there was where the Synoptics and John were written, or something to do with the date of composition, i.e., too early for John to matter? too late for John to matter?, but I haven't found a sufficient answer. As regards geography, the Synoptics and John weren't written in the same place to the same group but they all concern themselves with John. If we accept the existence of Q we find that the Jesus-Movement was concerned with the Baptist Movement quite early. If we don't accept the existence of Q we still have Mark written at a relatively early date, probably (60s.). The Gospel of John and the Gospels of the Ebionites and Nazarenes, as well as the Infancy Gospel of James, evidence that late first-century to early/mid-second century Christianities were concerned with John's legacy. So, it would seem that geographical and/or temporal matters related to the composition of these gospels doesn't quite explain Thomas' peculiarity.
But what if John's insignificance is theological? For example, in Thomas the "Kingdom of God" is less an imminent, physical, space-time political event to be anticipated as much as an inward, life-changing reality that has happened already (the same can be argued for the Gospel of John to an extent). So, maybe the idea of the eschatological/apocalyptic judgment didn't jive with the author(s) of Thomas? Regarding this, James D.G. Dunn suggests:
I find that this has a lot of explanatory power. John wasn't forgotten. John's preaching wasn't overlooked. Instead, as with other Gospels, Thomas minimized John's preaching where it was suitable to the Gospel's message. John's apocalypticism didn't jive with Thomas' realized eschatology, so John, and more so his prophecies, were redacted even further.