That's rather harsh, don't you think? All models have their limits and scopes, but that doesn't preclude them being useful in their own right. For instance, Newtonian physics simply can't cope with molecular-scale events, but it still gets used every day for the cases where quantum or relativistic effects don't matter. Likewise, phylogenetic classification is still a hugely useful tool within biology. The fact that it has assumptions and limitations merely defines it, rather than diminishing from it.