This is the (first) fundamental mistake of the article. The purpose of taxes is to raise funds for necessary services, as stated in steps 1 - 5. The only question is how to raise those funds fairly.
As soon as you start thinking about incentives and changing behaviors, the tax system suddenly has two purposes rather than one, and those two purposes can be at odds. Really, in a free (as in freedom) country, the government has little or no purpose in trying to guide behavior, except to prevent people from illegally harming others.
"Individual income taxes are bad because: They penalize people's initiative, hard work, savings, investing, and attempts to better themselves."
It's not a penalty, it's simply a fair rate based on ability to pay. Even under progressive taxation, you still end up better off by making more money. There would only be a "penalty" if the tax rate were 100% or somehow >100% for additional income.
The only thing that prevents people from bettering themselves is means-testing some essential service, such as health care. In other words, losing your health care or having it priced out of reach when you get a better job or start your own business. This is why we need single-payer. (And arguably government-subsidized higher education.)