There is a very easy way to sample a matrix that works if you understand that R represents a matrix internally as a vector.

This means you can use sample directly on your matrix. For example, let's assume you want to sample 10 points with replacement:

n <- 10
replace=TRUE
Now just use sample on your matrix:

set.seed(1)
sample(dataset, n, replace=replace)
[1] 1 0 0 1 0 1 1 0 0 1
To demonstrate how this works, let's decompose it into two steps. Step 1 is to generate an index of sampling positions, and step 2 is to find those positions in your matrix:

set.seed(1)
mysample <- sample(length(dataset), n, replace=replace)
mysample
[1]  8 12 18 28  7 27 29 20 19  2

dataset[mysample]
[1] 1 0 0 1 0 1 1 0 0 1
And, hey presto, the results of the two methods are identical.