Latine disco, p. 13
Cur mater Marcum verberat? = Why does the mother beat/flog Marcus?
Marcum verberat, quia . . . = Marcus gets beaten/flogged, because . . .
Am I right in thinking there’s no difference between active and passive in this case?
I probably should know what Latine disco means - but, alas, I don’t. 
No.
Verberat is active. In the second sentence, Marcum verberat quia . . . , the subject (presumably mater) is understood but not expressed, and Marcum is accusative, i.e., the direct object, just as in the first sentence.
Unlike English, subject pronouns need not be expressed, and are generally not expressed unless emphatic. Latin verb endings convey the person and number of the subject, so personal pronouns are generally not necessary to identify the subject.. (of course, if the subject is a noun and not a pronoun, the noun is expressed and is in the nominative case.)
Passive would be Marcus verberatur. The subject must always be in the nominative case, not accusative.
I think you are guessing rather than looking at the endings.
In the second sentence you have to understand mother from the first sentence so:
She (mother) beats Marcus because…
If this were a passive sentence the verb would be “verberatur” which I guess you haven’t got to yet. Dont worry about the passive until you get to it. I won’t confuse you unnecessarily by explaining further why the sentence couldn’t be passive.
I think you need to read more carefully p 13. All you need to know is explained there. Ask again if this isn’t clear.
Latine Disco “I learn in Latin” would be my take. Others more familiar with these materials, which I have only recently started looking at, will no doubt correct me.
Right, got that.
You are right - was again conclusion jumping, my favourite pastime. 
Thanks Hylander and seneca for clear explanations.
L