I don't even understand how regular money works... why does it have value and why does bitcoin have value?
Money originally arose due to a desire to trade more efficiently, just as language originally arose due to a desire to communicate more efficiently. Money has value just as words have meaning. Both are emergent properties, driven by natural human desires.
Note: This does not explain why any one particular currency has value, but rather why there exists some form of money.
Or how business charge more for the cost to buy something, how does it not end up in debt? When you charge more for the original cost of something. Service, work, knowledge, value. My microencomics class did not help me much, it would seem. (Macro is what I could have used too)
Don't worry. I'd bet many people don't understand this but are afraid to confess such ignorance.
There is value in owning certain objects (goods). A simple example would be a plumber fitting a $3 washer to fix a leak in your kitchen. We can easily identify the $3 of value in the utility of a dry kitchen. However, the plumber might charge $60 for this, a markup which occasionally confuses people.
As you rightly observe, there is value in certain kinds of labour, and the skill (knowledge) of the labourer plays a part in determining this value.
But the story does not end here. There is value in all kind of things: location (shipping), customer knowledge (advertising), risk mitigation, time (investing), et cetera. Businesses often work to unlock such efficiencies and, the extent to which they are successful is the extent to which they can profit.
To be confused by a factory owner profiting above the costs of materials, maintenance, and wages is just a more subtle version of being confused by the plumber's $57 markup.
A person slaves away digging a ditch, and someone hands him an address so he can get paid? As opposed to handing him money, or better yet food.
Suppose I want to employ you to dig a ditch for me (a full day's work). Could I pay you with 3kg of 1-day-old date and walnut cake and 20 freshly baked potatoes?
Also what happens when quantum computers become common place?
Quantum computers theoretically break certain cryptographic algorithms. Bitcoin may have to transition to newer algorithms as older ones fall.
What is this 21 million cap governed by?
A form of consensus. The 21 million cap is effectively part of the definition of Bitcoin. The full definition of "Bitcoin" is written as a piece of software called "Bitcoin Core". The analogy is weak, but you might consider why the English word "water" has the meaning that it has and how you might go about changing this meaning.