in this column: http://www.straightdope.com/classics/a960405.html
Cecil answers a question about late tax returns. In it, he states that “All penalties and interest are figured as a percentage of what you owe. If you owe nothing the penalty for late filing is zero”.
It is clear from the question and answer that this information is directed to individual tax payer returns. From my personal experience (related here), the answer was/is different for corporations, even if no taxes are owed.
This year, my corporation (a non profit under 501 C3) filed for an extension, and then filed the return about a month later than normally due (but well within the extension limit).
Some months later, we got a notice from the IRS that we owed some $900 in penalties for late filing, despite owing zero in taxes.
We sent a letter showing our request for an extension and the IRS eventually agreed that we owed nothing.