Rake is collected so the card room can make money, otherwise why run one.
Typically it is 10% up to $5 per hand, charity rooms do $6 max. At almost every room there is never a rake unless there is a flop seen (this was not always the case), the same for online rooms.
Tournaments will take a percentage of prize pool. Anywhere from 5% to 20%.
Some online rooms take less, the average is around $3 max per hand.
What does this mean? The higher limit games get raked less per hand in terms of percentage of the pot.
When you play pot limit games the pot is determined before the rake is taken out.
High limit games will charge a per/hour fee called 'time' instead of rake. WSOP
'time' is between $7 to $15 per half hour payed by all active players. Some really high limit games the players will decide that when TIME is due, whoever wins the next pot pays for everyone...these pots are in the thousands so it is quite insignificant for the most part.
When playing split pot games, and you know there is a high chance of splitting the pot, when you are heads up it is wise to check it down if the max rake hasnt been taken yet to avoid paying more. I feel that split pot games are not the best when playing cash, especially heads up play.
I never heard the term 'capping the rake', so not sure what you mean there.
How it affects the pots, well its a game of math. A $50 pot you really only win $45. A $100 pot you only win $95, a $10 pot you only win $9, etc...no rake if pot is under $10 (except online).
Hope this helps