Pinning means telling that node that the data is important and it should be saved. It's like pinning a message on Slack or Discord. This prevents data from being deleted in your node as you only have control over data pinned to your node. The difference between Pinata and Filecoin is that content is never pinned in Filecoin, only IPFS can pin things. Filecoin nodes do run IPFS in the background, but the process that does the pinning is IPFS, not the Filecoin miner.
See: https://docs.filecoin.io/about-filecoin/ipfs-and-filecoin/