Update 2019-08-27: this tool has reached end of life and seems no longer maintained.
All in all, I'd say your wish list for a gratis tool like that is quite long. In the last company I worked for, I was responsible for the maintenance of projects and I made myself familiar with metrics and code quality analysis. Below information is given on my knowledge of ~2 years ago. The only free tool I found that roughly matches your requirements is
ConQAT, the Continuous Quality Analysis Tool.
- analyzes Java, C++, C#, ABAP, ADA
- is gratis (Apache 2)
- integrates in Eclipse, so you can rename variables etc. as usual
- allows for analysis of architectural constraints and code clones
- works at least on Windows, not sure about Linux. It's Java-based, so it might work there as well if you don't need C# support.
- easy to use: well, it depends on what "easy" means for you. The metrics are built with a GUI, so basically, yes. You should have knowledge of metrics, though.
- graphical depiction of the functions: not something like IDA Pro, but e.g. with treemaps. It can also visualize the architecture at least down to class level.
- large source codes: I have no clue how large the source code of Linux is. It worked fine on a C# project with 130k LOC
Other notes (based on information 2 years ago):
- The tool is updated in irregular intervals, although the version numbering system suggests that there are 2 releases per year.
- It's hard to get support, unless you're willing to pay for it. I did not find a "community" that would answer questions.
- You can implement own information providers in Java.