It's a pain, surely this is something that you don't do, the user highlights "foo.com" and is instead given "http://foo.com. It's as bad as the sites that use Javascript to inject "read more @ http://bar.com...
It wouldn't be so bad if it was optional, but don't expect that of Chrome, oh no.
It also leads to an inconsistent experience, I'll quote myself: "If the URL you're using is http://website.com and you copy website.com, you get http://website.com, but if the URL you're using is https://website.com and you copy website.com, you get website.com. It not only messes with copying by changing what you copied into what it thinks you want, it's inconsistent with that guessing."