The issue was and is only with her use of a privately run SMTP server for her government job. There's three key problems, first off it avoids FOIA requests, secondly it can avoid other legal discovery, and lastly information was sent through it of a sensitive nature.
And before someone replies with "nothing was sensitive!" if that were true then why has the government redacted and withheld emails from the public? And retroactive classification is largely a myth, things inherit classifications from their source.
So for example if you attend a classified meeting and you or your staff take notes on that meeting, those notes are classified at the second pen touched paper. It doesn't matter than it lacks a classification marking.
And that's for a lowly developer job dealing with absolutely no classified information.
You'd probably still catch some flak but you might have enough power/influence to actually do it whereas if you're employee #42593 of a big company there's no way in hell you're gonna get your way.
Similarly, Clinton will probably get away with it. That doesn't excuse her behavior though. Might does not make right.
Hopefully she'll keep that character flaw in check as president, but I wouldn't be surprised if she didn't.
Personally, I think [email protected] would be a much better vanity email address than <myname>email.com.
Even if the only reason was to have a custom domain, I'm sure the State Department's IT team could point the MX records to a government-managed mail server.
The issue is that she was apparently told to use the .gov email address provided to her by her work, and she did this instead.
People have accused her of doing this for various reasons, but personally I don't believe there's evidence to show that she did this for any other reason than wanting to stand out and look special by sending mail from [email protected], and so that she could use her own BlackBerry.