The Viet Cong were recruited and trained by North Vietnamese cadre to help disrupt the democratic government of South Vietnam. They also were told that the United States forces were aggressors,...
For the very same reason the British army had trouble with the Swamp Fox (Francis Marion) during the Revolutionary War; for the same reason the US Army had difficulty with Quantrill's Raiders...
The Vietcong fought a guerrilla war based mostly from underground. They would attack and hide and ambush. This made it hard for the U.S. to fight them.