My parents who are currently here in the US for visiting are not able to go back due to covid-19 flight cancellations. Hence I would have to file for extension, but why is the fees not being waived as its not our mistake. The total fees is more than $500.
The I-539 fee is not a fine. The I-539 form is not primarily intended for the correction of mistakes. The I-539 is the form with which one applies to change or extend nonimmigrant status, and that is what your parents want to do. To make the application, they need to pay the application fee.
There is a fee waiver available, but it is only available to some filers of the I-539. Even if your parents are eligible to apply for a waiver, I would not apply for one without first checking with an immigration lawyer, because asking for a fee waiver could reduce the chance of the application being approved.