Why did Polar Express make me feel queasy?

It may be that you have fallen for the classic effect called the Uncanny Valley.

The reason those humans seem creepy to you is that they indeed look pretty much like real humans and not like exaggerated caricatures of humans usually seen in other animated movies. This first sounds rather paradox, but when looking at arbitrary animated creatures (like toys, talking animals or even artistically distorted humans) you don't care if they don't behave exactly like humans. But because the figures in the Polar Express look so much like real humans you realize even slight divergence from human behaviour much more. So the more realistic and human-like a figure looks, the more you expect it to behave exactly like a real human, and if it then doesn't, it feels kind of creepy to you.

This is kind of a subconcious process. You first see some pretty well visualized humans and instinctively think they are humans but then you realize they behave somehow strangely and inhuman and that difference in realism between visual appearance and animated behaviour is what makes you feel creepy. The linked Wikipedia article may provide some more theoretical insight into this effect (in fact it even lists the Polar Express as an example).

That may be the case because Polar Express is made using motion capture Technique, Which is not used in Shrek, Toy story etc. Motion capture techniques are generally used to present real emotions or live movements. Or may be the case that its animation is not made that playful as Toy Story or Shrek to make it more realistic. In general, Polar Express got good appreciation with mixed reviews but it received a cult following.

So it made this way on purpose and I think it's done to make it feel realistic.

Uhm. How about some of the action was a little terrifying for kids and some adults. (The close calls falling off the train, the Eller coaster ride, the breaking ice,etc) not to mention the creepy,prison escapee type elves.