Hola Goo

Yes, this is used idiomatically - there are lots of expressions that aren't literal to the English in contexts that are seen in basic levels, for example, when talking about the weather or when going shopping, to a cafe, to the doctor... 

We can't make specific lessons on every idiomatic expression I'm afraid, but when we do a gap-fill exercise about a specific situation/context we generally accompany these exercises with a list of relevant vocabulary/expressions that help understand the topic.

In this case we don't have anything specific for the "cafetería" but I've noted it down. 

Meanwhile, the way the person working at the cafe normally asks you what you'd like to have is by saying:

¿Qué le pongo? - literally meaning what do I put you? (that sounds really odd in English) 

And you would say:

Me pone un café y... literally You put me a coffee and... (still sounding horribly odd in English) 

But this is the way it's done in Spain and it's perfectly polite to say it. 

We are actually using the usted form of the verb "poner..." to express politeness. 

I hope this clarified it for you.

Saludos