My undergraduate senior project was on the interaction between breast milk and microbial ecology in infants, so I can appreciate the difficulty of protein phylogenetics in non eukaryotic organisms. I think it's still important to underscore that simply because whatever tree I get phylip to spit out doesn't reflect the true evolotionary history of the organism/gene/whatever, doesn't mean that 1)tracing the evolutionary history of an organism/gene/whatever is "bullshit" (whatever you mean by that) or that 2)the evolutionary history cannot be elucidated by other means. Phylogenetics can be used to discover gene fusion events and convergent evolution.