I don't know Ayer's work well enough to comment on what he had in mind, but here are a couple of general observations about the relationship between education and indoctrination. First, there are certainly some similarities between the two. There is a sense in which they do the same kind of thing, namely, they both aim to bring it about that the people who 'undergo' them come to adopt some beliefs and behaviours and give up other beliefs and behaviours as a result of their education or indoctrination. Also, both can fulfill a common function, that of training individuals to occupy the various roles (doctor, soldier, parent, priest, etc.) that people fulfill in the societies in which the indoctrination or education takes place. One central difference between them, I would say, has to do with the attitude that a student is allowed or encouraged to take towards what she is taught. Education gives a student at least some freedom to question what she isbeing taught (and in principle, perhaps, complete...

The label 'Continental philosophy' tends to cover an extremely diverse collection of philosophers and approaches, and there's a lot of disagreement about who and what exactly should be included. So I'll just recommend two books that I (as someone who works in 'analytic philosophy') found useful as introductions to some of the major German philosophers and schools. First, Andrew Bowie's "An Introduction to German Philosophy: From Kant to Habermas" is a great overview of many major German thinkers, especially in making clear how their views grow out of and are connected with their predecessors. David Couzens Hoy's "The Critical Circle" is a bit more narrowly focused on hermeneutics and the connection between philosophy and literary theory, but it draws together the work of German, French, and American philosophers and literary theorists in a way I found very helpful.

As an alternative to starting with a broad survey, you might also consider diving straight into a single work, such as Hume's "Dialogues concerning Natural Religion", Descartes' Meditations on First Philosophy , or Plato's Symposium . These (relatively short) classic works in the history of Western philosophy (and there are plenty of similar texts from other traditions and time periods) take you directly into central philosophical problems while being a treat to read.