While I'm not a clean- or a neat freak and certainly buy my handbags to enjoy them and use them and not keep them in a bubble, I like to think I'm careful enough with my nice stuff and don't abuse it.
I wouldn't put my bags on the floor in public places unless I absolutely had to, like in case of an emergency or something like that. But I do carry food in my bags. I make sure that it's in a tight lock container and preferably in a sealed plastic bag as well. Just for extra protection. Or if it's something that won't stain even if brought out of its packaging, like a banana or an apple or nuts I can just put it in a plastic bag and forget the container.
And of course, water gets put in there all the time. I don't like leaving home without having a small bottle of water on me unless it's a quick grocery run or something like that. But I try to keep the bottle vertically, just in case.
Makeup goes into a makeup bag unless it's a small bag and the only makeup I'm carrying is a lipstick. Then I just make sure the cap isn't loose. But powdery or liquid products have to go into a pouch.
And I wouldn't put anything dirty in the bag, no thank you. Like a dirty tissue. If I can't throw it out, a jeans pocket will do just fine.
I don't normally carry many pens and liners, but if I do, I use a separate pouch for those too. Not really for protective reasons, just because I don't like it when small stuff gets spread all over the bag. I prefer to keep small items in their personal pouches. If it's just a couple of pens, I make sure they're not automatic but have a cap and put them in the inner zipped pocket - all of my bags have those.
So far nothing bad happened to any of my bags, thankfully!