You can't configure it to trust any key (that would be a breathtakingly huge security vulnerability), but you can get SSL certificates for your servers, either self-signed (import/trust the root CA) or buy them from a trusted CA.
You can definitely set up an automated process without too much effort that generates new SSL keys for each server based on your own self-generated Root CA, and deploys them whenever a cloud server spins up. Then you just have to trust the Root CA on your FileZilla client and you won't get the popup.
You might ask "well how do I do that?" -- that'd have to be another question, and it would depend entirely on:
- Which operating system/version/distribution you're using on the cloud server(s)
- Which operating system you're using on the box that generates the keys (the "Root CA" box)
- Which FTP software you're using
- Which SSL suite you're using
- What sort of deployment/scripting/automation environment you have set up, and the mechanism for customizing it