When looking at node.js heap profiles, I find that it's really helpful to know if the code is busy and allocating memory (i.e. does a web server have a load?).
This is because the heap profiler takes a snap shot of everything that is in the heap at a the time of profile collection, including allocations which are not in use anymore, but have not been garbage collected.
Garbage collection doesn't happen very often if the code isn't allocating memory. So, when the code isn't very busy, the heap profile will show a lot of memory allocations which are in the heap but no longer really in use.
Looking at your flame graph, I would guess that your code isn't very busy (or isn't allocating very much memory), so memory allocations from the profiler dominate the heap profiles. If you're code is a web server and you profiled it when it didn't have a load, it may help if you generate a load for it while profiling.