Yes, that is on purpose. There were some security issues that were related to the implementation we used before where, under specific circumstances and with user's sharing a computer, it was much easier to unintentionally 'merge' a different user's Facebook account with someone else's Joomla user.
We're investigating a similar implementation (auto login) as an option for the next revision of JFBConnect. I can't guarantee it will make it in, but we'll definitely note that it's desired.