With the 1099 you are adding un-taxed income at the end of the year to your total income. The taxes on it have to come out of somewhere, and it does depend on your situation. Did you claim a lot of exemptions on your W-4?

My airline adds the bonuses into our pay, from everything I've seen, and are taxed right away. In that situation, paying more tax in the end is usually a product of what you claim, deduct, your bracket, etc..