Yes. All ForeFlight data is downloaded over a secure SSL connection. This includes the airport and navigation database, instrument procedures, airport diagrams, sectionals, and IFR enroute charts.
After a download is complete, ForeFlight Mobile performs MD5 checksum validations on the download data to ensure the data was not corrupted during the download. Additional pieces of the downloaded data are opened and tested inside the app. If any of the validation steps fail, the data is removed from the iPad or iPhone and the download is attempted again.