When we flew into Germany from other Schengen countries (Frankfurt from Barcelona this year and Munich from Venice last year) we had to go through passport control, but we did not have to go through passport control on the highway between Portugal and Spain. Can someone enlighten me?

You always go through ID control for European domestic flights (even in the same country), it's about air security, not about immigration.
(and you can get random ID controls anywhere)

And you could also experience the same ID checks at road borders or on trains in recent years as well in my experience - not common but possible.

Even inside countries, like in France, there are at times road checks where papers are scrutinized - in fact i saw a picture in a local French paper about Customs police stopping a Dutch van and searching it with dogs for drugs. Schengen is great but it doesn't mean countries don't or can't do further checks they wish.

There are very few borders in Europe and you can often drive from one country to another without seeing customs (paranoid Britain being an exception). Getting out of Andorra can be a pain too since people buy tax free stuff there.

I live in France and still use UK plates on my car. Rarely the local Gestapo (offices in Rouen) stop me and I forget all my French while they waste my time.

Were your flights terminating in Germany, or were you connecting through Munich/Frankfurt to a non-Schengen destination (US, etc)? If the latter, then you were going through passport control on your exit from the Schengen zone.

Poster norween said "You always go through ID control for European domestic flights" - not so, depends hugely - recent flights FRA-HEL, HEL-CGN, CGN-CDG all had no immigration or other check on arrival.

Your flight from Barcelona to super-busy FRA probably arrived at a gate on a concourse where flights from non-Schengen airports also disembarked, so the whole lot of you had to be checked. I would think that in a place like FRA it must be almost impossible to segregate arriving Schengen from non-Schengen flights, at least much of the time.

I wrote 'you go to ID (for identity) control' not to immigration.
I fly minimun twice a week in Europe and always have to show a valif id with my ticket when checking (and sometimes a second time when boardind) - this check is not on arrival but on departure

(i hit the send button too fast) : the second ID control (when boarding) is sytematic when there is only airline staff a the checking place (this 1st one is not not what a call a passport control)

Thanks to all. I think Wally Kringen has the right explanation in this particular case. It _was_ a formal passport control with men in booths who stamped the passport as opposed to the boarding controls where one shows a passport as identification along with a boarding card.