Little Shino didn’t understand friendship. The people he was surrounded with were his rowdy classmates, nothing more. He preferred to keep to himself and his bugs – not really distancing himself, but not opening up to anyone either. It’s only until he’s put onto a three-man team does he learn what it means to have friends.
It’s the first time he’s had to work together with others to such a degree, co-operating on missions and training and putting his life in someone else’s hands. It’s the first time he’s allowed others to get under his skin, have them probe around, and perhaps to his surprise, find acceptance in them.
Despite all their clashing and misunderstandings, Shino considers Naruto a dear friend too! And in the moments where it counts, Naruto does try to include Shino and actually thinks he’s really strong. Shino feels such a strong connection to his comrades, so it upsets him when he’s not included or can’t be present to fight alongside them. In a way, his grudges are a reflection of the importance he places on bonds.