The company considers getting you to and from your base a benefit. They add the cost of your travel to your paycheck, usually 2 or 3 months after the month you traveled. Then all the taxes are computed and taken out of you pay. And the the cost your travel is deducted from your pay.
Simple math example. Say you earned 100 dollars and you are paying 25% in taxes. So you'd see $75 on your paycheck. Now say you had $10 in imputed income. Atlas would add the $10 to your 100, figure the tax withholding as $27.50 and then subtract the $10 from your paycheck so you'd receive $72.50.
It's not sales tax. The way around it is to live in base or jumpseat to work and get your own room.