Are freelancers automatically disqualified?
Absolutely not - actually, it’s a good thing. It shows you have initiative, you are a self-starter, and you can be given additional responsibility beyond “code this” (since, as a freelancer you also have to manage your time, your business, finances, legal issues, etc).
In regards to the pet project - it’s an application you built for you. You weren’t paid by someone else to do it, it was something you wanted to do - an idea you fleshed out from step one and if you made some money off of it that’s okay as well, but not really a factor.
The point is: most places are looking for passionate developers, not drones that are going to come in, do their work, and go home. When I hire someone it’s because they are passionate - if others listened in on a conversation they would think we are talking about work, when in reality we are just talking about something we enjoy: developing. Every passionate developer I’ve known has pet projects. Some examples from this community: Derek Allard (Bamboo Invoice), Phil Sturgeon (PyroCMS), Dan Horrigan (FuelPHP) - all successful pet projects they developed because they wanted to.