Is there a tool (e.g. Matrix) that will allow me to find a zero penalty airfare between two cities, regardless of the class of travel?

Momondo will like you filter out Basic Economy as a class of service. That will at least kill off the inflexible tickets that often carry change fees if you can change them at all.

Within standard economy, you'll have to read the fine print by airline. Most of my typical airlines will allow you to freely change or cancel the ticket with no fees - but you're left with flight credit that you have to use within a year of ticket purchase.

If "zero penalty" to you means fully refundable, you usually have best luck on the airline's website, as some airlines will allow you to add refundability to a discounted fare as an add-on for less than buying a full-Y ticket would cost.

I always start at Momondo just to get a vibe for the market and then go to airline sites when I've honed in on good options. Ultimately, I almost always buy from the airline directly.