It seems counter-intuitive to me that Winston Churchill would have been voted out of office at the end of WWII. He had just shepherded Great Britain through an incredibly difficult period and emerged victorious. Why then was Clement Attlee elected to Prime Minister at the end of the war?
First things first; judging by the phrasing of the question, I am assuming that you are somewhat unfamiliar with the Westminster system of government, and thus do not know that the Prime Minister is not elected to the position known as 'Prime Minister.'
The Prime Minister is appointed by Her/His Majesty, and chosen from among the elected Members of Parliament. In practice, the head of the largest party becomes Prime Minister, either at the head of an absolute majority of MPs of their own party, or as part of a coalition composing >50% of MPs.
Thus, while Churchill himself was still massively popular, the Conservatives as a party lost 189 seats, ending up at 197 to Labour's 393. EDIT: However, there is still some correlation between the success of a party, and the popularity of its leader, so it's pretty safe to assume the Conservatives would have lost even worse if Churchill had not been their leader.
The 12% swing from the previous election is the largest recorded in UK history. Partially, this was because the Conservatives had been in government since 1931, and thus were facing fatigue from the electorate, and blame for the troubles of the 1930s and early war. Labour, meanwhile, had become the face of the Beveridge Report, and thus the face of the proposal for a welfare state. They were bolstered in the popularity of this platform by fears of a return to 30s style unemployment, and by a perception of socialism as efficient, due to the positive view of the USSR given by their defeat of Nazi Germany.
Polling-wise, Labour had been in the lead since 1942 at least, and thus, while Churchill expected the Coalition government of the war to continue for longer, Attlee said no in '45, and forced an election.
TL;DR: While Churchill himself was extremely popular, the Prime Minister is, in practice, the head of the largest party, and not someone elected specifically to be PM. In 1945, a host of factors had made the Labour Party under Clement Attlee more popular than Churchill's Conservative Party, and they won a parliamentary majority, placing Attlee as Prime Minister.
"Coalition government of the war"? How did that coalition work and with which parties?