I think because some years ago (in PRL) bottles were made only from the glass. And now mostly alcohol is in glassed bottles. Other bottles are from the plastic - so we don't call them "flaszki".
BTW. "Flaszka" come from german "Flasche" = butelka.
Walkinthedog, it doesn't have anything with education of your parents. But with development of the language - it is natural thing that often name which described something else in the past changed meaning, e.g. swastika.