The Like button can be set to like any URL you want, as long as it's part of the application's Site or Base URLs. Since you're using a subdomain, just make sure the Base domain is set to "domain.com" and it will work for your main page (domain.com) and your sub (sub.domain.com).
This will take a little bit of effort though, as you'll have to manually set each Like button on the subdomain to point to the main domain's URL. This can be done in the module itself or in the { JFBCLike} tag using the href parameter.
In the 3.2 release, we'll make this a little easier for you as we'll be adding the ability to set the Open Graph tags on each page. These tags let you specify the canonical URL, image, description, and other data regarding what is being 'liked' when clicked. Once this is implemented, you'll be able to add these tags easily (hopefully) and have the URL point to the root domain instead of the subdomain. For more specifics on the Open Graph tags, should you have the interest in coding something now into your site (to automatically strip the subdomain from the URL for example), see the Facebook page below:
developers.facebook.com/docs/opengraph/
It will take some effort either way, but hopefully we'll be providing the tools soon to make it a little easier.
Good luck, and hope this helps!