Yes, but when you compare the numbers, McCain was the one who had the biggest shortfall by far. In 2004, Bush received 2,859,768 votes and Kerry 2,741,167. So far, McCain has 2,464,104 versus Obama's 2,662,951. Thus McCain had 400,000 less votes than Bush and Obama just 180,000 less than Kerry.
McCain was a deeply flawed candidate. If you nominate the party's maverick as your standard bearer, there are political consequences. McCain spent most of his time campaigning against his own party. Loyalty begets loyalty.
Correction: Obama received just 80,000 less than Kerry.