Just to spell it out - there are three (main) reasons why we would want capital gains taxed at a lower headline rate: 1) Capital gains are already taxed at the corporate level. People seem to intuitively understand how this works at the dividend level (dividends are paid with post tax dollars), but if you do the math, it works precisely the same with capital gains. (Please note: Tax incidence is complicated. Not all…
1) Sure, but effectively all income is multiple-taxed. Suppose I run my own business, and am paid by a consumer with their money that they earned as wages. If I turn a profit, I then pay taxes on that income. By this logic, I shouldn't have to pay taxes, because the consumer that paid me was using after-tax dollars, so taxing my income from them would be double-taxation, right? The double-taxation argument is simply not very-compelling because there's no one true wellspring of money; if there were, you'd just tax the source and call it good. But reality is way more complicated than that, and money is always taxed multiple times as it moves around the economy.
2) I don't think you're correct about there being empirical evidence of capital gains rates affecting those things. For example, see http://www.slate.com/blogs/moneybox/2012/01/19/capital_gains.... As far as I know, there's no credible empirical evidence that cutting capital gains rates deterministically helps investment or saving, or that raising them hurts those things. Sure, you can pick and choose examples with those outcomes, but you can also find plenty of empirical examples where those effects didn't happen. It's totally misleading to act like that's a settled question in economics.
3) He's paying more in taxes because he ended up earning more money. So yes, he deserves to pay more in taxes than Sally, because he earned more money. Otherwise, you could easily say "Sally decided to work part time and made less money than Fred. Does hard-working Fred really deserve to pay MORE in taxes than Sally?" Yes, yes he does; unless you really think that a poll tax is a good idea, even a flat-tax advocate would have to argue that someone who makes more money should pay more in taxes.