It's not that it's implemented poorly. It's that 1) the federal government collects multiple kinds of taxes out out of your paycheck. Social security, medicare and regular income tax are different. Income tax rates are progressive while the payroll taxes are flat but capped at a certain amount. 2) Additionally forty-two states have income taxes as do dozens of local municipalities. Consider that they also don't treat residents and non residents alike.

Consider a couple who live in New York City, where one partner works in Connecticut and the other works in New Jersey. There are potentially 6 different entities collecting income tax there.

That being said - fully agree - tax filing software should be free for everyone.