Samneric's fear can be traced back to chapter four when they first witnessed Jack painting over his face with clay and charcoal:
"Beside the pool his sinewy body held up a mask that drew their eyes and appalled them. He began to dance and his laughter became a bloodthirsty snarling. He capered toward Bill, and the mask was a thing on its own, behind which Jack hid, liberated from shame and self-consciousness."
The highlighted sections indicate the effect the mask had not only on the other boys, but also on Jack. The boys were intrigued and horrified at the same time. The mask changed Jack and the mask was something behind which he could hide. It provided Jack freedom from guilt and self awareness, it made him unconscionable, he could do whatever he wanted when he had painted it. The boys distress at witnessing Jack wearing the mask made them imagine that his laughter was a bloodthirsty snarl. The boys were thoroughly frightened and intimidated, so much so that Sam And Eric felt pressured to obey Jack's command.
"'Come on! I’ll creep up and stab—” The mask compelled them."
It is clear that Sam and Eric fear the savagery that wearing the mask brings about, that it changes those who hide behind it. They have now seen it with Jack and are not keen to be confronted by their fears again. In chapter 11, the twins voice their fears:
“He’ll be painted,” said Sam, timidly. “You know how he’ll be—” “—he won’t think much of us—” “—if he gets waxy we’ve had it—”
Later in the chapter we learn that the boys:
"... understood only too well the liberation into savagery that the concealing paint brought."
They are clearly afraid of the consequences brought about by the wearing of "war paint". The twins realise that the 'savages' would have no qualms to hurt them. We later learn that their fears are justified for Piggy gets killed and they are captured and tied up.
Ralph refuses to have their faces painted because, as he says:
“ ... we aren’t savages.”
Ralph's primary objective is rescue. He therefore wishes to maintain order and get the signal fire going again. If he should become a savage himself, all hope would be lost, there would be complete anarchy and they would never be rescued.
“The others nodded. They understood only too well the liberation into savagery that the concealing paint brought.” Eric again suggests painting themselves and Ralph yells “No paint!” He screams at them that they need smoke." (pg 206)
Samneric are afraid of what the savages in warpaint will do to them. They are afraid of the evil which has taken over the boys in Jack's tribe. Ralph refuses the paint because it does stand for savagery and he wants to try and keep the "civilized" order that he has tried to create through the whole story.
Samneric realize that when Jack and his tribe are wearing warpaint, they are liberated from acting civilized. Their fear is how the tribe will act when they are painted. Ralph says that he, Piggy, and Samneric must not paint their faces because he wants so badly to maintain a civilized way of life for them. He realized that if they become like Jack and his tribe, there will be no chance of rescue.