It was actually later revealed by Ilana that the person in the cabin was not Jacob.
Exiting the cabin, Ilana informed Bram that Jacob was not there, that he had not been at the cabin in a long time and that someone else was using it. She then ordered the others to set fire to the cabin. The group departed, leaving the structure to burn.
She further states that he hasn't been there in a long time and that someone else has been using it, therefore her desire to burn it to the ground. This is proven when on Locke's third visit to the Cabin, Christian Shepard is there with Claire. At this point we know that MiB is Shepard's father on the island (his ability to take on the forms of the dead), which would imply that he is the one now using the Cabin.
It is heavily implied that this someone is indeed The Man in Black (MiB) impersonating Jacob. It is not a surprise that MiB has been manipulating people just as much as Jacob in order to win his side of the Game between the two of them.
I believe Ben says this is Jacob because it is later revealed that Ben has never seen Jacob until the night MiB manipulated him into killing Jacob. So he would say this is Jacob because he saw the strange occurrences with Locke on that first visit. His bewilderment and expectation that no one would actually be there would lead him to believe that it was Jacob when it was not.
It should be worth noting that the producers/writers have not explicitly stated that it was indeed MiB inside the cabin and they have yet to reveal this at all, nor I don't think they ever will. But all the episodes involving the Cabin and what we know of MiB points to the extreme possibility of him being the one that Locke and Ben saw inside the Cabin.