Getting a job is all about connections, connections, connections.

First of all, as explained here, job boards (at least the big ones) are not an effective way to get jobs. Connections are. Furthermore when you're showing up to a job prospect through connections, issues like the one above about resume filtering become much smaller - the connection can point those facts out.

Secondly you'll have to accept that there are a lot of dysfunctional organizations out there. Stories like Anne Learns to Recruit are not far from what actually happens. So you can't be hired at some places. That's life.

Thirdly you have to become OK with this problem. You can fail 100 times without grief, so long as you succeed once. There are far more jobs that you're not qualified for than you are qualified for. As long as you can find one that you're a fit for, this isn't a problem. And you're more likely to find that fit if you can retain an upbeat opinion through it all.