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Probably WorkSpaces is not designed to be active 24/7. Desktop CPU usages are also usually much lighter than server usages.

The windows EC2 machines are also designed for web traffic (IIS servers). I suspect these machines will still get traffic but not at the volume of a web server.

Maybe the impending EC2 price drop (predicted by many in light of the new Google cloud pricing) will bring it in line.

They just announced the new pricing [0]. It's much cheaper, but still about 2x the price of the WorkSpaces. The only difference I can see is the local storage: 4 GB SSD on EC2 vs. 50 GB on WorkSpaces. I have to assume WorkSpaces is using a spinning HDD in that case.

[0] http://aws.amazon.com/ec2/pricing/effective-april-2014/

it's probably priced assuming 40hrs/week usage, not 168hrs/week usage.