You can use the !
operator to basically make any TRUE FALSE and every FALSE TRUE. so:
D2 = subset(D1, !(V1 %in% c('B','N','T')))
EDIT:
You can also make an operator yourself:
'%!in%' <- function(x,y)!('%in%'(x,y))
c(1,3,11)%!in%1:10
[1] FALSE FALSE TRUE