So you have setup your Metadata Service Application (including the content type hub url), you configured the proxy (making sure to check the consume content type checkbox), and you have published your content types! So everything is working right? Wrong.
What site did you use as the site collection root? If custom, what was the site used for your template? Turns out that not all site definitions have the TaxonomyFeatureStapler, including the Blank Site. This feature is required to work with the Managed Metadata service.
There is a powershell command to add the missing feature: Enable-SPFeature –Url “http://sitecollection” -Identity “TaxonomyFieldAdded”