- The Zohar (Bereishis 73a) says:
כד הוו זכאין ישראל אקרי ארעא על שמא דא
ארץ ישראל כד לא זכו אקרי ארעא על שמא
אחרא ארץ כנען
"When Israel was worthy,
the land was called by their name,
'Eretz Yisrael." When they were not, it was called by a different name, 'Eretz Canaan.'"
Given that most of Tanach was written in response to the failings of the Jewish People (see Nedarim 22a: "had the Jewish People not sinned, they would have been given only the Five Chumashim and the Book of Yehoshua"), then that might explain why indeed "Eretz Canaan" is the prevalent term.
- Radak (to Ezek. 17:4) also writes that it is called "Eretz Canaan" in order to highlight a derogatory contrast. He starts by explaining that "Canaan" literally means "merchant" (as in Hos. 12:8 and Is. 23:8), and continues:
וכן היתה ארץ כנען בטרם בא ישראל אליה
כי היתה ארץ שוקטת ולא היתה עובדת לשום
מלך אחר... אבל אחר שבאו ישראל לארץ
כנען היתה נותנת מס ועובדת מלכים אחרים
בסורם מאחרי השם
"The Land of Canaan, too, before the
Jews came to it, was a peaceful
country, not subject to any other
king... But after the Jews came to the
land of Canaan, it had to pay tribute
and be subservient to other kings,
when they stopped following Hashem."
- And Yalkut Shimoni (beginning of Parshas Shelach) says that it's called Eretz Canaan to remind us that (a) we didn't inherit it by our own merits, but because of the Canaanites' wickedness (as in Deut. 9:5); and (b) the one merit that we do have going for us is that of Avraham and Sarah, who were respectively 100 and 90 years old when Yitzchak was born; the gematria of כנען is 190.
Other than that, though, there are also some positive reasons given for this designation:
The Canaanites deserved to have the land named for them, because (some of them) left voluntarily rather than oppose the Jews' entry. (Bamidbar Rabbah 17:3)
Our physical world is called "Eretz Canaan" (Ohr Hachaim to Gen. 23:2, citing Zohar Bereishis 80a - although I haven't found it there, but in Midrash Hane'elam 122b). He doesn't elaborate, but I think I recall seeing an idea (probably somewhere in Chassidus) that the Torah calls the Land by this name because it is a prototype of what we are to accomplish: to take the "land of Canaan," in both the specific and the general meanings of this term, and turn it into a holy land.