Boxer is the hard working cart horse who is very adaptable to the new philosophy the Napoleon institutes. In fact, Boxer comes up with a maxim to accept Napoleon's rule, Napoleon is always right, and I will work harder. Like the sincere members of society who believed in the the ideology of socialism, were probably the most annoying to the establishment.
"In the end, once Boxer's health fails and he is no longer able to work, Napoleon sends him to the horse slaughterer. In Orwell's tale, he represents the common working class who unwittingly accept their base existence, because they believe by hard work they will get ahead and that their leaders will protect them. Boxer's lung trouble seems to refer to Orwell's own bouts with tuberculosis."
Boxer is a true believer, he works so hard that he becomes old before his time, thereby becoming useless to Napoleon. The fact that he must get rid of him poses a serious problem for Napoleon, because he does not like the idea of drawing attention to the fact that he must send him to the slaughterhouse.
This flies in the face of the ideology that Animal Farm was built on that all the animals will enjoy a peaceful, relaxing retirement in the grazing field. Napoleon shows the animals, very early on, that retirement for any animal who outlives his usefulness is not going to happen.
Napoleon likes to keep his real purposes veiled, secret, so getting rid of Boxer poses a problem, which highlights Napoleon's real intentions and this must be covered up immediately by Squealer, the chief propagandist.
I'd be interested in knowing what led you to this question. I can't see any reason why Napoleon would be threatened by someone who never asked a question, who exuded loyalty, who was a great worker ... he never seemed like a threat to me. Of course there is always the possibility that a figure as central to the Farm might have tried to lead a rebellion against Napoleon, but that is very unlikely. As pmiranda suggests, the only problem he ever presented was when it was time to "get rid of" him. But even that wasn't a great problem. With Squealer there to create a reality, that the knacker's wagon wasn't what everyone saw it was but that it was an old wagon that needed to be repainted, and with the animals seeming willingness to believe just about anything, even this wasn't much of a problem.
This concept is at the core of the book. Reality isn't as real as we would like it to be (each of us, for instance, has an opinion about George Bush and Barach Obama, even though we really don't know them and only know what someone, probably with an agenda, has told us), and the price of freedom remains "eternal vigilance."
[See the article below for a more detailed presentation by Orwell himself.]
napoleon feels threatened by boxer because he is the farm cart horse and he feels whatever boxer says should be done no matter what