I've run across this in the past; I agree it's confusing. When a user runs a workflow they expect the workflow name to be the name they see in the Kepler title bar, which is the filename. Right now it causes difficulty and confusion in WRM/provenance, but I imagine it's going to and already has come up in other places. Even if the title bar showed the workflow name, a user searching for this workflow at the OS level will struggle if the filename is different. And vice versa, if a user renames a workflow with the OS and begins to think of it by this name, they will struggle to find it via workflow name searches within Kepler systems. And yes, there will be added complexity once we're using kars more frequently and e.g. a user renames a kar filename from the OS.
If there were no such thing as a workflow name stored inside the moml (and refactoring was done) this confusion could go away, a new user's assumption could be correct: workflow name == filename. My impression of similar features in other programs is that they're rarely used (e.g. Word's Document Properties => Title).
All that said, I think when this discussion has taken place in the past, there were strong reasons brought up for keeping workflow name and filename two distinct things, not the least of which is that a significant amount of work would have to take place--e.g. a clean soln would probably mean changing the ptolemy moml format.
The provenance module used to allow configuration of the workflow name, but the group decided to remove that to simplify things. Right now afaict there is no way to do so. If we add a way, imo it should be extremely obvious.
Another soln to this particular problem is simply for WRM to display a filename column to search against instead of workflowname, but I believe the group disliked that idea since it subverts the desire for the prominence of workflow name.