We *nix nuts often think that *nix is the best, but we also often forget that we didn't come to this conclusion of someone else's volition. We came to it because we learned it for ourselves. In general, the first psychological reaction of "do this because I said so" is "screw you." You won't "get them to connect the dots" if that's what you're blatantly trying to do. They will do it of their own volition, however, if you just be your enthusiastic self, and talk about why you like this feature or that. When they can apply the skills you teach them to their own projects, they will be hooked, but the key is that they have to do it.
If they're fresh to the *nix terminal, or *nix in general, start slow, and, for the students' sake, consider doing just rote labs at first. The major ins and outs of the terminal are many and varied, so covering them all will be difficult and overwhelming. Instead you might introduce them to the shell by way of a simple set of exercises (programming or otherwise) that build on each other week-by-week. As commands are needed, introduce them, but no sooner; any sooner and you risk overwhelming them. The first CS course has historically provided an incredible learning curve, not due to the conceptual bits you want students to learn, but to the outside learning that we take for granted once we know it. Small things, like the directory structure (i.e. strange/new/arcane compared to Windows), all the command line flags, and the excess of information that comes way too fast.
Skilled teachers introduce their subjects like a conversation: they don't blow their wad in the first 2 sentences. They start slow, introduce a concept, munge it, then build from there. Introducing the maze of power and concepts that is the shell really can't be done in one single class. Getting "them to connect the dots" is not within your control. Just as you can lead a horse to water, but you can't make him drink, so too is it with your students. Have a project into which they can sink their teeth, like building C/C++ program with a few different files, or writing a shell script to collect data from 5 of their classmates computers via ssh. When they can take ownership, they'll connect the dots on their own.
Finally, remember that this is an introductory course, so they likely will not know what you may think they should. They are not stupid, just uneducated on this subject; remember that they're there to change that.