Short answer: yes.
Longer explanation: Bones are useful because they give muscles something to act on. As a body increases its muscular strength, the pressure and stress the muscles place on bones increases. To counteract the force of the muscles, the body will enrich bones to both increase their size and density so the muscles themselves don't break the bones.
Bones are also used as a general storage for extra minerals when the body has excess. Anyone with a lot of extra nutrition will deposit more of the minerals in the bones, making them more dense and more difficult to break.
Then there's the padding of muscles and fat to consider, relieving blunt trauma by distributing force over a greater area. Even without the padding, a fresh bone from an athlete or larger person in good shape will be harder to break than an nonathletic or skinny person. Notice I left out obesity; there is a limit to what the body can store in the bones without the muscles working them. Obese people, sadly, break a lot of their own bones due to their massive frames because they are often not compensated for by bigger/denser bones.
Science? Yeah, science.