it appears that you need to learn more about how wifi works. Here are some quick pointers.
There are several types of wifi APs (Access Points) in the real world. Here are the most popular.
1) completely open - does not require a password or any type security certificates. This type is growing increasingly rare. This used to be the standard setup of in home wifi, but it is now #3.
2) webpage acknowledgement - these type requires the end-user to click sometype of button or give some type of password or give some type of security code -- all the variations have a wepage. I have found this to be the most popular type of system, in places like Starbucks and MacDonalds.
3) WEP/WPA or similar - this type requires some type of some type of password/passphrase or give some type of security code. This type of system requires that you fill some type of popup form on your laptop or similar system. Note: this type system is usually consider more secure and is also used for public access. I have found it used in motels, coffee shops and fastfood places (like Jack in the Box)
4) certificate based - This type of system is usually implement in corporate environments where easy of access is required and no password is required.
5) Any combination of #2, 3, & 4.
FWIW: when the Arduino Yun is an AP it is type #1 - when connected to the Internet.
Here is a reference article from wikipedia. It lists about a dozen security protocols, but there are in fact more that 50.
To finish up, there is no one software system available that can handle all the different security methods available. However, I have heard there is one hacker software that can break into the most weak wifi systems - I don;t know the name of it.
Best of Luck,