Here is an example which shows that full-rank $C$ is not always sufficient to ensure that $W\cdot C$ has full rank. Both $W$ and $C$ have full rank, but $W\cdot C$ does not.
$$W = \begin{pmatrix} 1 & 2 & 3 & 3 \\ 1 & 1 & -4 & 1\\ -3 & 1 & 3 & 2\end{pmatrix} $$
$$C = \begin{pmatrix} 1 & 1 & 1 & 1\\ 1 & 1 & 0 & 1 \\ 0 & 1 & 1 & 1 \end{pmatrix} $$
$$W\cdot C = \begin{pmatrix} 1 & 2 & 3 & 3 \\ 1 & 1 & 0 & 1\\ 0 & 1 & 3 & 2\end{pmatrix} $$
In $W\cdot C$, the first row is the sum of the other two rows.
I'm confident that any number of rows and columns can give a similar counterexample with at most one 0 per row of $C$.
NEW: There are some values of $C$ such that $W\cdot C$ has full rank whenever $W$ satisfies the conditions. The simplest example is the identity matrix. More generally, if $C$ has a unique transversal (set of 1s, one per row, in different columns) then $W\cdot C$ has full rank whenever $W$ satisfies the conditions. It is plausible that those are the only examples, but I'm not sure about it.
NEWER: I didn't write a detailed proof, but I believe that if $C$ doesn't have full rank there is always a counterexample (i.e., one can find $W$ of full rank such that $W\cdot C$ is not of full rank). Reorder the rows of $C$ so that a row full of 1s, if any, is first, and there is a linear relation $R$ that defines the last row in terms of earlier rows. Now we construct $W$ out of $C$. The first $N-1$ of rows of $W$ are those rows of $C$ with a tiny random negative perturbation of every entry. With probability 1, those $N-1$ rows of $W$ are linearly independent. The final row of $W$ is constructed from the final row of $C$ thus: Where $C$ has 0, enter a random negative number in $W$. Where $C$ has 1, apply relation $R$ to determine the entry in $W$ (since the first $N-1$ rows were only perturbed by tiny amounts, this will give a positive value). Now I believe that with probability 1, $W$ has full rank. However, $W\cdot C$ satisfies the relation $R$.
SO FAR (always assuming the given conditions on positivity and structure):
(1) If $C$ has less than full rank, then there is some $W$ of full rank such that $W\cdot C$ does not have full rank. (But some other $W$ of full rank might give $W\cdot C$ full rank.)
(2) If $C$ has a unique transversal (which is an example of full rank), then for every $W$ of full rank, $W\cdot C$ also has full rank. This can be generalised to the case that some $n$ columns of $C$ have a unique transversal.
(3) If $C$ has full rank but is not in case (2), I don't know the answer.
The example at the start of this answer is in case (3), so it is not true that full rank $C$ is always enough to give full rank $W\cdot C$.
EVEN NEWER: Here is a theorem. It applies only to the square ($N=n$) case at the moment and extending it to the rectangular case will need some thought.
Consider two properties of $C$:
(A) For every $W$ which has a positive value wherever $C$ has 1, $W\cdot C$ is nonsingular.
(B) $C$ is nonsingular and has permanent equal to the absolute value of its determinant.
Theorem. (A) and (B) are equivalent.
Proof. [(B)$\implies$(A)]. Transversals correspond to permutations and have parity even/odd. Condition (B) says that $C$ has at least one transversal and all transversals have the same parity. This means that all the non-zero terms in the expansion of the determinant of $W\cdot C$ have the same sign, so their sum is not zero.
[(A)$\implies$(B)]. Suppose $C$ has an even transversal $M_e$ and an odd transversal $M_o$. Form a matrix $W_e$ like this: put a very large positive value where $M_e$ is, a tiny positive value in the other places where $C$ has 1, and a random negative value where $C$ has 0. Form $W_o$ in the same way using $M_o$. Now, $W_e\cdot C$ has positive determinant, and $W_o\cdot C$ has negative determinant. Since the determinant of a matrix is a continuous function of the matrix entries, there is $W$ which is a convex combination of $W_o$ and $W_e$ such that $W\cdot C$ is singular.
In the non-square case ($N<n$), we can generalize (B):
(B') Some $N\times N$ submatrix of $C$ is nonsingular and has permanent equal to the absolute value of its determinant.
Then the implication (B')$\implies$(A) holds, since $W\cdot C$ is full rank iff it has an $N\times N$ non-singular submatrix. The remaining question is whether (A)$\implies$(B') holds too.