There is no good reason. But now it's scary to change it, since there could be places where we assume that usernames can not begin with a lowercase letter. There is task https://phabricator.wikimedia.org/T28396 about this. Although folks are complaining about it, it seems that no one has proposed a patch. (As long as the default is still to user capitalized usernames, I don't see why we couldn't have an option to allow lowercase ones.)
For example, one case where we assume usernames can't be lowercase is in some "shortcut" URLs for special pages. URLs like https://en.wikipedia.org/wiki/Special:Contributions/Matma_Rex and https://en.wikipedia.org/wiki/Special:Log/Matma_Rex will display the edits/logs of an account, but URLs like https://en.wikipedia.org/wiki/Special:Contributions/newbies and https://en.wikipedia.org/wiki/Special:Log/block have special meaning (and the edits/logs of a user named "newbies" or "block" couldn't be accessed like this). In this case it's harmless (you could still access them using the form), but there might be assumptions like this in more important places.