It's common for end users to complaint about the domain prefix that they have to use at the login for a SharePoint site (windows authentication). And it frustates users when they can't login with their usernames and have to be reminded time and again about the domain prefix.
One alternative is to use UPN or User Principal Name to be used as login. UPN is nothing but a suffix that is added after a username which can be used in place of "Samaccount" name to authenticate a user. So lets say if your company is called Microsoft, then instead of Microsoft\Username you can use email@example.com at the authetication popup.
Adding an UPN to active directory is straight and simple (only requirement is the access to global catalog server). http://support.microsoft.com/kb/243629