What's the meaning of " It is just that"

Solution 1:

The phrase It is just that cannot usually be understood without reference to the context in which it is uttered. It often follows an expression of negative polarity. Google examples include:

It is not that you do not have options, it is just that you cannot see them.

Dogs do not actually prefer bones to meat; it is just that no one ever gives them meat.

The main problem is not that most people don't know the common sense thing to do, it is just that they don't do it!

So, the sentence "It is just that the specific policies and practices associated with transnational liberalism are not the same as globalization tout court" could have been preceded by something like:

I don't think you are wrong about the essential aspects of transnational liberalism. (It is just that the specific policies and practices associated with transnational liberalism are not the same as globalization tout court.)

In such contexts the expression functions as an indication that whatever was stated or implied before may well be true, but misses the main point. And the main point is what follows the It is just that ... .

Solution 2:

At least in the various examples given, "it's just that" is an informal and, perhaps more to the point, diplomatic way of saying, "but".