Tthe way i understand it:
there are usually 3 biological enzymes in a typical enzyme pill:
-Lipase breaks down lipids (fats) and other water-insoluble substances
-Amylase breaks down starches and complex sugars into simple sugars
-Protease breaks down protein chains.
when you take a birth control pill, the hormones don't belong to a class of molecule that need to be broken down by the natural enzymes in your stomach/small intestine, so therefore they do not need to be taken with replacement enzymes. The same theory applies to antibiotics.
HOWEVER- the efficiency of hormonal birth control pills can be altered by certain antibiotics, and it is important for the doctors to have a complete list of meds (including hbc pills) before they prescribe anything, and additional methods of prevention might need to be used while on an antibiotic course.
Any liquigel caps containing oil/fat-soluble drugs (e.g. aquadek and marinol) should probably be taken with enzymes.