Use 'protrude' to emphasize the visibility of something sticking out physically. The broken bone protruded from the skin.
Pro Tip 2/3
Beyond Limits
It often implies something extends so much that it replaces or overshadows what's around it. A tree branch protruded above the fence, blocking our view.
Pro Tip 3/3
Object Interaction
Think of how the protruding object may interact with its environment. The shelf protruded too far, causing people to bump into it.