At the very least Cubby benefits from a mature infrastructure that LogMeIn sits on. From what I've read they have numerous geo-balanced (akamized) data enters, each with multiple levels of redundancy and overlay routing, i.e. the whole nine yards. Also being a publicly traded company makes them more accountable and well-behaved.
On the other hand AeroFS appears to be an extension of an offline/LAN utility to the cloud, whereby Cubby is the other way around. They had the client-server setup with p2p connectivity and extended it to the LAN context.
AeroFS treats the cloud as just another peer. You can use it, if you want, or you can just use your own devices. Heck, you could install AeroFS on an AWS box backed by S3FS[1] or equivalent and have your own private cloud :)
On the other hand AeroFS appears to be an extension of an offline/LAN utility to the cloud, whereby Cubby is the other way around. They had the client-server setup with p2p connectivity and extended it to the LAN context.