The default VLAN and the native VLAN are really two different concepts that are often mixed up because they are often the same VLAN, but they may not need to be.
VLAN 1 is the default VLAN (meaning not configuring a VLAN on a switch interface will leave it in VLAN 1). The bad guys know that it exists on your network, unless you take steps to remove it or not allow it. Some vendors even require VLAN 1, as do some versions of spanning tree (STP versions may require it as both the default and native VLAN). Because it is the default VLAN, a lot of people also use that as the management VLAN for their network devices. All of this makes it a prime target for the bad guys.
Because frames on trunks are tagged to separate the frames into VLANs so the frames can be placed in the correct VLAN on the other end of the trunk, that means that one VLAN could be untagged and still separated, and that is called the native VLAN. Because VLAN 1 is the default VLAN, it ends up as the native VLAN by default. Depending on the vendor and version of spanning tree used, you may be able to change the native VLAN to a different VLAN.
Avoiding the use of VLAN 1 and not having a native VLAN makes it just that much harder for the bad guys, and it is a simple thing. Cisco recommends not using VLAN 1, restricting VLAN 1 from trunk links (
switchport trunk allowed command), and not using a native VLAN on the trunks, meaning that all the VLANs on a trunk would be tagged, and there would be no VLAN 1 frames. In fact, you should restrict trunks to only allow VLANs that are required on the other end of the trunk link, but a lot of people just let it default to allowing all VLANs. Also, you should disable VTP by putting the switches into transparent mode. There is also a command to tag the native VLAN, which means that you really do not have a native VLAN.
Remember that VLANs were bolted onto ethernet after the fact, and there really was not the huge problem of people hacking into networks and trying to cause problems back when the standards were created.