The 65-year-old has a 19-month-old son, Zachary, with his partner David Furnish, 49.
In an interview with the UK's Radio Times, Elton said, "At school other children will say, 'You don't have a mummy'.
"We've come a long way, but there's still homophobia and will be until a new generation of parents don't instill it in their children."
Zachary was conceived using a donor egg and born via a surrogate in 2010.
Speaking about his son's home life, Elton said, "It's natural for him. He calls me 'Daddy' and David 'Papa'."