This is one case though where that lack of understanding leads to the right conclusion. The average user is giving up nothing by losing the right to run arbitrary code, because they never were running arbitrary code.
JavaScript is allowed on iOS and Android already. So if Goole or Apple do not allow you to run some scripting language you want then the reason is not security(the sandbox and permissions should be enough and if is not enough then it means the sand boxing is a lie).
... which is, unfortunately, a weakness of F-Droid's own making (for the right reasons!). Because they don't do stat-tracking on users, they don't have numbers. So Play Store is able to claim "1 billion active monthly users" (as of 2015) with some certainty, F-Droid can give an approximation and a shrug.
"The average person is giving up nothing by losing the free speech, because they never were saying anything."
Change your point a bit.
People are fine with giving up Freedom because they were never really Free in the first place.
Circular reasoning is sucha seductive fallacy because it'll fit any use case like a glove.
I may have the freedom to bash my neighbor's head with a rock, but they have the same freedom to do the same to me. This isn't as useful as the freedom to sleep at night, so we voluntarily give up this freedom.
Reframing to the topic at hand: if the freedom to mutate the code on my mobile device makes it more likely that I'll get pwned by some clever social-engineering than the odds I'll improve my quality of life by tweaking some behaviors on the phone, then it's entirely rational for me to give up that freedom. And, indeed, millions of phone purchasers annually make that decision.