I've got a few possibilities:
1) Apples were one of the first domesticated fruits, and originated in west Asia/Turkey... not far from the middle east where the Garden of Eden is believed to be located. If a biblical historian had to guess what type of fruit it really was, there's a good argument that it really was an apple.
2) Historically, the word "apple" has been used as the generic name for any foreign or unknown fruit in western civilization.
3) Apples play a big role in Greek mythology. Renaissance artists had two favorite themes - Greek/Roman mythology and Christian biblical scenes. So, surprise, they often made the most infamous pieces of 'fruit' from the bible, into an apple.