Do I have to pay penalties associated with not filing state income tax if I was due a refund?

Since you didn't file a return your state tax authority did so for you. This is most frequently referred to as a substitute for return. In preparing a return for you, you were not given the advantage of statuses and deductions which you may be entitled to claim. This is why the tax is so high, compared to your expectation of receiving a refund. If you file a return showing no tax owed within the time frame set forth for your state this amount should be substantially reduced. It may, however, not be eliminated - I believe that MA like CA has a penalty for failure to file, if you were required to file, even if you would have owed no tax.