Answer: you don't want pc$rotation, it's the rotation matrix and not the matrix of rotated values (scores).

Make up some data:

> x1 = runif(100)
> x2 = runif(100)
> y = rnorm(2+3*x1+4*x2)
> d = cbind(x1,x2)

> pc = prcomp(d)
> dim(pc$rotation)
[1] 2 2
Oops. The "x" component is what we want. From ?prcomp: "x: if ‘retx’ is true the value of the rotated data (the centred (and scaled if requested) data multiplied by the ‘rotation' matrix) is returned."

> dim(pc$x)
[1] 100   2
> lm(y~pc$x[,1]+pc$x[,2])

Call:
lm(formula = y ~ pc$x[, 1] + pc$x[, 2])

Coefficients:
(Intercept)    pc$x[, 1]    pc$x[, 2]  
    0.04942      0.14272     -0.13557