On PokerStars for example, they take $.05 for aver $1 hand, up to $3 per hand. So in the big games they're pulling in $3 per hand which amounts to a lot when they play their 60 (or whatever) hands per hour.
5% is a significant number. It's more than credit card companies charge stores per transaction.
And even at low stakes that's significant. Look at it this way; a credit card company will charge a card holder a 15% annual interest rate. That is, if you owe $100 you'll be paying 15%, or $15, after a year (actually more because it's compounded). A lot of people call that 15% a ripoff. But when a site charges 5% rake, it's instantaneous, and it repeats every single hand. That adds up quickly. Every 20 rakes hands they're winning one averaging a pot profit. That's 3 or 4 average pots per hour per table. (PokerStars has over 20,000 tables running now, though I don't know how many are tournaments)
As for the 100% or 110% or whatever bonuses, those have to be unlocked. Basically, to unlock it you have to play enough that you're paying that much back in rake. So essentially a 100% deal means that you're playing rake free for awhile.
But even when you're playing
"rake free" while until you match your initial deposit, sites make money off you. First, you attract more players who are not receiving deposit bonuses. Second, the
poker site has your money and can do whatever it wants with it until you cash your check. That means they can deposit it and get interest, or invest it. We're talking about hundreds of millions of dollars in funds that they can draw interest on.
Let's say like
Zachvac, you deposit $100 and turn that into over $10,000. Now you're playing $200NL and keep $10,000 in your account at all times to stay well rolled. Well, that $10,000 would get 3.5% or whatever if he stuck it in a bank. That's $350 he's missing out on each year he keeps it on PS. And you know who's keeping that $350 in interest.

Plus, big depositors (multi-million dollar deposits) get special, higher interest rates.
Again, that interest is in addition to the thousands that they made off his pots.