Ahmad,
A Native VLAN is the vlan that is used should a trunk port receive an frame with no explicit VLAN tag. I will give you an example of how I used Native VLANs in the real world:
For many of my locations, users have a single network connection to their desk. They use both a VOIP phone (not Cisco 
), and a PC. Both of these devices use the single network connection. The connection goes to the VOIP phone, and the computer plugs into another port on the phone. The VOIP traffic is on a separate VLAN than the PC data traffic.
To get this to work, we have to configure each port as a Trunk and allow both the VOIP VLAN and the PC Data vlan on the switch port. We configure the switch so that the native VLAN is the PC Data and the tagged VLAN is the VOIP. The reason for this is because the VOIP phone can read and understand 802.1Q tags, while a PC has no idea what that is–in fact the extra information in the 802.1Q tag makes the PC believe the frame is mal-formed and it will discard it! By configuring the Native vlan as the PC Data vlan, this means the PC gets an untagged frame, so it knows what to do with it. At the same time, the PC is on the correct VLAN.
Does that make sense?