I hear what you are saying:  How is the individual mandate a tax?

Justice John Roberts wrote that if the mandate is read as a command – “you must buy health insurance” – that it would be unconstitutional as beyond the powers of the federal commerce clause.

Here is the text of 26 USC Section 5000A:

“(a) Requirement to maintain minimum essential coverage

An applicable individual shall for each month beginning after 2013 ensure that the individual, and any dependent of the individual who is an applicable individual, is covered under minimum essential coverage for such month.”
It certainly reads like a command. It uses words like “shall,” a typical command word.
However, the section goes on to say:
“(b) Shared responsibility payment

(1) In general

If a taxpayer who is an applicable individual, or an applicable individual for whom the taxpayer is liable under paragraph (3), fails to meet the requirement of subsection (a) for 1 or more months, then, except as provided in subsection (e), there is hereby imposed on the taxpayer a penalty with respect to such failures in the amount determined under subsection (c).”
In other words, a person does have the option to not to buy health insurance. If they do, their taxes will be raised by a penalty in order to help offset the amount we (the other taxpayers) have to chip in to cover uninsured medical costs every year.
Thus, the result of noncompliance is not a criminal penalty, but a tax increase.  And that is how the “individual mandate” is a tax, and not a command.