I disabled my ssid on my wrt54g linksys router and this caused me to disconnect from internet. I was able to reconnect eventually. My question is I read disable the ssid makes my internet more secure but how do you do this and still be connected?

I think what you're looking for is to not broadcast your SSID which is different than disabling it. In terms of security it really only protects against the casual passerby from seeing your SSID if they're nearby. If they are intent on knowing what your SSID is then that is easily accomplished. The best method for securing your wireless router is to insure you have current firmware and you are using a strong key and use WPA2.

Also keep in mind that when you suppress broadcasting your SSID you will need to enter that information manually on your wireless device because the device (say laptop) won't be able to see it without explicit definition.