You aren't the only one. I thought the same thing while reading this and felt the mechanics behind the atoms' movement was easy to understand and explain in what the article seems to suggest is difficult to explain. Perhaps either the bucket example was a bad one, not explained correctly as to what was difficult to understand, or Newton didn't understand certain aspects of the physics of atoms at the time. I'm not a physics or history expert, but it seems like a failure of the article to make the problem clear, not you.