I think the two biggest factors are stiff bearings and the wind resistance of bulky clothes.

You can immediately feel the stiffness of a cold bike as you kick-off on your early winter morning ride. the bike doesn't even coast as easily as it did in summer. Theoretically, the ride will improve as the bearings and grease warm up, but I don't think that happens effectively in below freezing temperatures, especially with the hub flange and spokes to act as cooling fins.

Grease in rotating bearings at very low temperatures turns the grease to a consistancy of soap or spun honey.

Also, clothing makes a HUGE difference in wind resistance. We are essentially kites on our bikes. The bigger the kite, well you get the idea.

I think the stiff tire hypothesis is off-mark because hard tires are supposed to give less rolling resistance and make for a faster ride.