Good question. I've reread the ending and I think what bothers me is that I interpreted the new Daneel/Fallom "being" to be a new threat to humanity. Trevize, who has such accurate intuition, has always distrusted Fallom and the last line makes him seem particularly creepy. Daneel now wants to overcome the Laws of Robotics so they won't inhibit him any more, yet to me that is what makes him altruistic. Now he is stepping into the unknown.
Consider an older story, "The Evitable Conflict", featuring Stephen Byerly, a humaniform robot who became a world ruler during Dr. Susan Calvin's time. He was a good ruler - not due to superior intelligence or mentalics - but because he was guided into right actions by the 3 Laws of Robotics. He was also humble and more than willing to seek advice from other people.
Daneel (started by Giskard) is much more manipulative. He doesn't truly seek humans' advice in what they want to do, he makes decisions and then alters the minds of people around him to fit those decisions. He keeps altering his brain to be more powerful, but he continues to be secretive. By the end, he went from my favorite character in the Asimov stories to an all-powerful God-like being controlling the fate of the universe.
Further, in his attempt to do what is best for "humanity", he has changed what "humanity" really is. It is implied that he altered the early Gaians to be more pliable to him, but I think he should have found a solution that didn't keep everyone subverted to his will.
But upon further reflection, maybe Daneel wasn't meant to be the "outside threat" hinted at during the last few pages of the book. The Solarians, with their powerful mentalics which have been ignored by all until now, could be a great threat to the rest of humanity if they chose to do something besides hide on their planet. Maybe that is what is meant by the last line, " 'After all', and here Trevize felt a sudden twinge of trouble, which he forced himself to disregard, 'it is not as though we had the enemy already here and among us.'
And he did not look down to meet the brooding eyes of Fallom-hermaphroditic, transductive, different-as they rested, unfathomably, on him."