Disadvantages - a lot of apps aren't great because they're written by amateur developers and don't go through the same strict quality/screening process as apps submitted to the app store.
The reason why they're better is because they don't have to conform to Apple's guidelines. Also most of the developers that submit apps to the app store are amateur developers. Which is why a lot of the apps Apple sells are worthless.
if i have already registered my credit card with itunes and want to jailbreak would that make a difference
It doesn't matter at all if you have registered your card with iTunes.
Think of jailbreaking this way.
When you jailbreak your phone, you enable non-apple approved software to be installed, and gives you access to the phone. That is the only thing that jailbreaking does.
One of those new pieces of software is Cydia. Cydia is like another appstore where you can get other programs, ones that apple doesn't have their paws into.
That means the expected cost of jailbreaking is $2.99 (.01 x 299) for me.
Tell that to the guy who lost his $299 iPhone. Personally, the expected cost of jailbreaking (although there's a 1% chance of there being a cost) is $299. If you lose your iPhone, are you personally going to be paying $2.99 for it? Maybe the average cost over 1000 users will be so, but on an individual basis the argument is simply not true.