Thank you for your response.
I've already figured out what i'm doing wrong.
The problem was not initialization. I did this after the calculation was done, so the flat source regions were already initialized.
The problem was in the way I tried to create LocalCoords object.
I'll leave here the instruction for those who will meet the same problem as me.
So, if you want to get the flux value at the given coordinate you should do the following:
xc, yc, zc = (x coordinate you need), (y coordinate you need), (z coordinate you need)
loc_coord = openmoc.LocalCoords(xc, yc, zc)
loc_coord.setUniverse(geometry.getRootUniverse())
loc_coord.setCell(geometry.findCellContainingCoords(loc_coord))
fsr_id = geometry.findFSRId(coords=loc_coord) - 1 // geometry is your openmoc.Geometry class instance