Yes, it will update on its own. Just give it a chance. If it still is not updated within the next few days, you can always go into (from home) settings->applications->manage applications, find "Market", tap it and then tap the button "clear data". Go back into the market, choose your Google account if you have more than one, approve the terms and see if that helps speed things along.
I do have to say that every time I factory reset a phone I tend to get the new market within hours, so it's unusual that you do not have it yet, but I have had to wait once or twice for a few days. It's not that big a deal to me - as long as I can get to the apps that I need, I don't care about the version.