PowerFolder automatically tries to connect over HTTP if a direct connection via TCP or UDP is not possible. This means PowerFolder can still connect when running in a firewall-restricted environment where only "web-browser" Internet connection is available.
In case you only have access via a HTTP Proxy, please make sure you have entered the correct settings under Preferences/Network/Proxy settings.
Tunneled traffic will be encrypted with state of the art encryption. Nobody except the source and target computer can read the contents files you are exchanging.