Toddler not liking mommy (BL)

My son, who’s two, is on a full on Daddy kick. Every morning when he wakes up he cries because I’m the one who comes in to get him up. Today he said, “I don’t like Mommy.”
Up until now he has always loved me the best (which felt good!).
In my worse moments I’m making it mean that I’m losing those baby years when he loved me best, and he’ll never want to spend time with me. Intellectually I know that he is just learning to assert his independence and separation from me, and of course that’s good. How do I get that knowledge into my head and heart? (Or do I just accept that it hurts and that’s okay??)