Seems to me that "teaches you how to think" does not necessarily imply instilling habits of thought. I would interpret that (say, in the context of Art History) as:

• Supplying you with some maps of unknown to you territory
• Giving you some tools to explore and map the territory further
• Pointing you towards some well-worn tracks as "default" ways of thinking about the issues involved

The habits of thought are not involved in all of this -- it's more of a broadening-your-horizons exercise.