The hill country of Canaan is the central highlands of present day Palestine and Israel. Pharaoh Tutmosis III conquered the entire Levant (present day Israel, Palestine, and Lebanon) at the battle of Megiddo.  However, the Egyptians knew that strict control of the hill country of Canaan would be difficult and it was not really necessary at that time.  Tutmosis sought to control the passes to protect the Egyptian homeland from invading armies.  The important areas were the seacoast and the Jordan River Valley.  The hill country remained autonomous.

While the story of the Exodus talks of an organized movement of a large population to a specific destination, refugees do not migrate in such a manner.  The Amarna refugees probably fled to several different locations.  In the case of Moses, Midian (present day Arabia along the Gulf of Aquaba) was his likely destination. Other possible destinations for the refugees are modern Ethiopia, Yemen, and Jordan.  However, the hill country of Canaan is where they successfully reorganized themselves as a community.  Why were they more successful there? We cannot say for certain, but we can make some educated guesses.

During the Amarna era, Egypt had a large Semitic population.  Many of the Amarna refugees were probably Semites themselves, and Canaan was a place with a familiar language and culture.  Furthermore, the Semitic population was primarily in Lower (northern) Egypt, which is a relatively short journey to Canaan.  Even for non-Semites, the hill country was a reachable location that was outside Pharaoh's control.

Finally, we can't rule out the possibility that the Jewish communities outside of Israel, like Yemen and Ethiopia, could actually be traced to Amarna refugees!  This may sound far-fetched, but no one really knows how these communities began.