The tone of the article seems to be slightly rushed and frustrated and leads me to wonder if the author just received unexpected news from his accountant.
One example:
Using 2013 tax rates and assuming that the taxpayer is single:
Individual Federal income tax on taxable income of $90,000 (ignoring personal deductions/exemptions/itemized deductions, etc..) that the example taxpayer in the article might have to pay if they were a 50% partner/member in an LLC:
Roughly $18,493 (less than 21%)
Corporate Federal income tax on $100,000 if you and your partner had a C-corp instead and took 40k salaries then left $100k in the company.
Roughly $22,250 (About 22%)
But then if you end up not spending that money because you made a boatload of cash the next year and want to take it out:
$3,337 (15% capital gains)
leading to a rough total of $25,587 (over 25.5%).
You might look at this example and say "hey that's just a few %" but as the income in question grows, so does the gap.
Edit: The real reason startups might end up as corporations is for the beneficial tax treatment investors can receive as holders of small business stock (1202, 1244).