Why are the animals uneasy about Napoleon's dealings with Mr. Whymper?

They're uneasy because it seems to betray everything they believe and everything they've ever worked for. The whole point of driving Mr. Jones from the farm and carrying out the Animalist revolution was to show that the animals could stand on their own feet, to make a success of the farm on their own without any assistance from the hated human oppressor. So when Napoleon starts establishing contacts with a local lawyer called Mr. Whymper, the animals are understandably less than comfortable with the arrangement. But Napoleon doesn't really care about Animalism; to him, it's simply a means to an end, a way of consolidating his own dictatorial power. And he'll do anything he can to maintain and increase that power, even if it means forging relationships with human society.
What Orwell is doing here is satirizing the way in which numerous Western intellectuals—"useful idiots" as Lenin famously called them—fell over themselves to offer support to the Soviet Union, despite the appalling suffering the regime inflicted on its own people. Mr. Whymper symbolizes these shameless apologists for the Communist regime. For his part, Napoleon, like Stalin, is only too happy to establish good relations with those who are supposed to be his ideological enemies to consolidate his iron grip on power.