I have the same problem saving - due to permissions, and Automator doesn't tell me where it is trying to save it other than HD, and all permissions in my /user/Library for both Automator and Workflows are RW for user (according to GetInfo). Automator won't even give me a choice where to save a workflow so if it's choosing to save in / I can see why I don't have permission.
What else can I look at to try and save a workflow and not get permission violations and how do I make that happen?
Automator (V2.5) doesn't have "Preferences..." which is normally in the app's menu, to see where the default location is, and Automator->File->Open looks in HD at the root file system '/', and if I look using Open in /user, "Library" doesn't even appear, and in Finder I'm currently showing all files. (An Automator script I wrote back in ?MtLion? - I'm now on Yosemite.)