The TCP/IP connection can be over Internet, or with PAN over Bluetooth, or WLAN ad-hoc/infrastructure connection, anything really.
That is the beauty of having it working top of TCP/IP. Also security can be obtained with well tested tools (ssh, VPN, SSL, ...)

Well, ok, the more elegant way would be to use UDP/IP so there would be no need to setup session before the cut/paste, but synergy could be a very good starting point and just develop the UDP/IP support to it. Working on existing "standard" and especially when it comes to security, IPsec would be the right way, except with Bluetooth, IPsec could be forgotten first for now because BT has its own encryption (do not transfer passwords though).

Don't know about bluetooth that much (yet), is there some profile which would be more suitable to be used for UDP/IP than PAN.

If UDP/IP support is built to synergy, broadcast could be supported also, so any device in the neighbourhood could grab the flying clipboard-message. But only those, which valid passwords, could decrypt the message and make sense of it. Broadcast support probably won't be high in priorities, but there should be a place-holder for it and in mind when developing.