Both are possible in different contexts. "I'll meet you at the store" - At a point, where you want to meet. "Where's John?", "He's in the store" - In an enclosed space. John is in the area of the store. Also for example you can say with 'at' and 'on'. "Someone's at the door." - Meaning they are close to the door. "There's a poster on the door" - Meaning a poster is on the surface of the door.