Velasco (2014, Philosophy of Science) and others have suggested recently that the "tree of life" is not really a tree, and therefore the idea is at best, a "model." At the roots, among bacteria, that is undeniably true, but most systematists study multicellular eukaryotes, and there, the paradigm seems less threatened. However, the "gene trees/species trees" literature seems to be trending towards questioning the singularity of the treeness of phylogenetic relationships of all sorts of taxa. I wonder what people think about this.
For individual homologic DNA strands ("genes"), as long as they are not hybrids by crossing-over events, a tree is still the best way to illustrate the history of that strand. Whether that DNA strand crossed "species" barriers or duplicated, is a complete different aspect. Gene trees are useful (networks might be useful to illustrate homoplasy though). The interpretation that a gene tree is corresponding to the phylogeny of a species, is something different.
In plants, hybridization and polyploidization appear to be quite important in some groups (but so is asexual reproduction where hybridization is ruled out), so strict tree-thinking would be against the current knowledge. Generally, I would think, it's a matter of scale. If you look at relationships of (sexually reproducing) individuals on a species level, then trees might not be the best way of illustration (incomplete lineage sorting, hybrids, polyploids etc.). On a broader scale (deeper nodes/higher ranks but with rather few DNA strands/genes), many hybrids (incongruent constellations among the gene trees) already died out. Thus, relationships appear to be more and more tree-like, because those hybridizations are harder to detect. If you go on a finer scale with many DNA strands (genes), then you might find more hybrids again, because some hybrid genes are still floating around in the population. Since most phylogenies today are based of rather few DNA strand relationships and "traditional" speciation is also important, trees are prevalent in literature. I wouldn't be surprised if this will change when phylogenetics switches more and more to phylogenomics.
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