Using transporters to beam out waste seems like a waste of power. As such they would render human orifices like the vagina, penis and anus useless, and I find it utterly stupid to stop a bodily function simply because you are lazy ... plus while I think it's possible to use transporters for extracting waste out of the body, I don't think it's done or reccomended.
If the toilets are similar to anything we have today (which is a possibility, but not a definitive one) then I would sooner say all of the waste that is left behind is 'flushed' away (or a similar 24th century Trek analogy of the term) to the specialized system that breaks everything down to the most basic usable components (probably like being converted into energy and basic atoms for later use ... and that's the only viable usage I see of the transporters for waste extraction ... or it's more likely the waste goes through a certain area in the system that breaks it down to atoms and energy).
Essentially speaking, the 24th century relies more on matter conversion technology ... changing energy into matter and back again (replicators are the same in this aspect and they only need to be programmed with items they can create, or if you want to make something of your own, you must provide the formula for it ... and anything else is done through conversion of energy into matter or specific material structure necessary to create virtually any object/meal/whatever ... provided of course it doesn't go beyond the replicators ability to do so and the energy requirements aren't astronomic for a specific item).
Energy is used to power every system on the ship and SF can convert it into matter.
Recycling saves power, and no one really cares from whos anus their dinner came out.

That is because in the end your dinner will essentially taste/smell of what you wanted and nothing else with a flavour of poop or urinary liquid will be present.
This is why SF ships basically have an abundance of power ... well, for the most part that is.
The Malon for example were presented with the idea of recycling which would essentially solve most of their problems with their waste which is on top of everything toxic and they rejected it.
The waste problems practically never happens on a SF ship due to the systems in place that would use/reuse anything available in all ship systems.
SF - safe for the environment.