I think I will give this one a shot. You are right in having a hard time understanding all this. However, it is the best we have at the moment.
1) The entire SSL system seems like an enormous flaw by centralising the trust of the entire world in very few points (the certificate authorities). I don't understand this well but it seems to me that if the CA could be hacked, it would be a security breach that would cascade to the entire world using that CA at the top of their chain.
The Certificate Authorities goes through great pains to protect their infrastructure to prevent exploit. However, exploit has occurred. Look up the history of DigiNotar for example. But the reality is that the CAs are not just selling certificates. They are selling trust. Few people remember the days when buying a cert took weeks and required faxing (yes faxing) electric bills and other identifying forms to prove that you really existed. Today, you do a host validation and poof, you have a cert. So the reality is yes, the root CAs can be hacked. But if they are, the hope is that they will discover it quickly, invalidate the root which thus invalidates all certs. I believe that not one of the CAs wants to live through that scenario. In most cases, they will be out of business. Recovering from a breach like that would be almost impossible.
2) If a CA's public key is available to everyone, what keeps people from getting the content of a valid certificate and then making a program encrypting that with all kinds of keys and trying to decrypt it with the CA's public key until the day the public Key decrypts the encrypted content?
The nature of the public key is that it is exactly what it says... public. It doesn't matter who knows it. It is only good if the corresponding private key remains valid.
3) How can you setup your own CA server 100% securely?
Technically, you probably can't. Well, unless you become a root CA. I can not imaging the cost and time to make this happen. Now, that does not mean you can not create your own CA. Plenty of businesses do this. Why pay a 3rd party for all your certs when most are used for internal services? Roll your own and then you can issue as many certificates as you would like. Ah, but only devices with your root CA will explicitly trust the certs. And as csound1 already stated, nothing is 100% secure.
At this point, using the SSL infrastructure is the best solution we have for security. After all, look no further than Apple's App Store. Every developer is issued a certificate that is embedded in apps and installers. If that developer is found to be nefarious, Apple revokes their certificate. The revocation means that any internet connected device will immediately fail to run the app or installer. This is the ultimate kill switch in the sky. It is backed by certificates.
So while you should expect exploit and the possibility of hacking, your best plan is likely to pick trusted vendors. Picking the cheapest SSL provider may not be the best solution for you and your business. Pick a partner that you trust. Then trust that they will hold up their end of the bargain and keep those private keys safe.
Reid
Apple Consultants Network
Author "El Capitan Server – Foundation Services" :: Exclusively available in Apple's iBooks Store
Author "El Capitan Server – Control & Collaboration" :: Exclusively available in Apple's iBooks Store
Author of Yosemite Server and Mavericks Server books