Sure you can get the rhombohedral lattice parameters by peak matching in Fullprof program. But Fullprof will give you only hexagonal lattice parameters which you have to trasform to the rhombohedral cell. But the transformation is easy.

Scatter is a software from University Hamburg. It is simple to use and you can find lattice points easily.

In case you know the phase and only need a refinement PowderCell is still a nice tool since theer you can also change easily into the different settings or subgroups.

WinXPow is very easy to use, but commercial and only hexagonal. but you should be able to transform the cell.

WinCSD is free, a little more difficult to use though, it allows rhombohedral settings