Wounded King has already dealt with what rRNA is.
The protein meaning what it makes such as bone, tissue, organs, etc. right?
Those things are composed to varying degrees of proteins, yes, but proteins are much important for their other roles. Nearly all enzymes are proteins, and enzymes control which reactions happen when and where in the body; receptors are proteins so the way that cells respond to signals is controlled by proteins, and a lot of those signals are themselves proteins.
So looking at a bunch of organisms to build a tree based on rRNA is still the same method that as used prior to genetics based on morphology likeness and differences.
Firstly, we were talking about molecular clocks, not constructing trees. Molecular clocks are used to
date splits not construct trees.
Secondly, yes, there's some similarities in the way that trees are constructed based on morphology and genetics but the genetic approach is much better because (a) genes contain much more information than morphology; (b) the identification of different characters in morphology is subjective and arbitrary whereas the identification of differences in genes is objective and consistent and (c) genes can still be reliably compared even when there is almost no morphological similarity between two organisms.
A morphological comparison of Archaea, Bacteria and Eukarya would suggest Archaea and Bacteria are closer to each other than either is to Eukarya; but the genetics of rRNA revealed that Archaea are closer to Eukarya than they are to Bacteria. As our knowledge of the cell physiology of Archaea has increased this finding has been widely supported.