I discovered an issue which was documented in a blog by Wictor Wilen regarding using a blank site template and fell into this trap myself as there seems no point turning on lights on a site collection that will only be used as a content type hub (Turning on lights would allow anyone to think it was somewhere to put content right?).
As I’d already created the site collection with a blank site I wanted to understand what exact feature was missing.
So the problem is that if you create a subscribing site collection blank root site then published content types aren't replicated to the newly created blank site collection. I’d made sure all the timer jobs related to the content hub we’re run but no luck.
I stumbled across a post which didn't specifically relate to the issue to but I had a feeling I was in the right place.
The feature is called TaxonomyFieldAdded and by querying a blank site you will notice this is not enabled whereas on a Team Site it is.
So I enabled the feature by running the following command from PowerShell:
Enable-SPFeature -Url "<enter url here>" -Identity "73EF14B1-13A9-416b-A9B5-ECECA2B0604C"
Almost instantly the published content types appeared in the blank site collection.