Buneary likely has lower than normal base friendship because it is a Friendship evolution. According to the Pokedex, both Buneary and Lopunny are cautious creatures.
When it senses danger, it perks up its ears. On cold nights, it sleeps with its head tucked into its fur.
An extremely cautious Pokémon. It cloaks its body with its fluffy ear fur when it senses danger.
If you were already a high-strung Pokemon and some trainer came and stuffed you in a Pokeball, you probably wouldn't trust or like them very much, so Buneary has lower than normal friendship.