It is done for two reasons:
First to avoid confusing the general with the specific, e.g.:
"There are three common terns in Northumberland, Sandwich Tern, Common Tern and Arctic tern, and five common gulls, Black-headed Gull, Common Gull, Herring Gull, Lesser Black-backed Gull and Great Black-backed Gull"
Second, because it introduces uniformity of treatment, so that you don't have to work out whether a species 'should' or 'shouldn't' be capitalised depending on the etymology of the name. Otherwise you have to go through the silliness of having to capitalise some (e.g. birds named after people or places) but not others, which makes the species concerned appear to be of unequal taxonomic status (even though they are equal)
Michael