Yes, absolutely. In fact, we use Ottomatik to manage and backup Ottomatik itself.  

Our systems leverage enterprise-grade configuration management technologies and processes which are proven and secure. Which include secure encryption and communication channels.

The agent that runs on your server generates its own encryption key pair, and our servers do the same.  They conduct a key exchange to verify each other's identity then communicate through encrypted socket connections thereafter.

Additionally, any sensitive information you provide (such as a database password etc) is stored in an encrypted state which can only be read by the Ottomatik web application and your particular Company account.