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WEP, WPA and other wireless encryption methods operate specifically between your wireless client, or computer and your WiFi access point (WAP). When data from your computer gets to the access point or gateway, it is no longer encrypted and it is transmitted over the public Internet to its destination. The only exception to this is when you're using SSH, SSL (commonly employed when you make a purchase on the Internet) or VPN, in which case it is still encrypted.
While using an advanced tool like WPA will protect you to a degree from intruders, you might also consider additional protection techniques such as VPN.