What is wrong with this reduction from vertex cover to binary programming? I am trying to polynomial-time reduce the decision version of vertex cover to the decision version of binary programming.  Here are the problem statements.

Vertex Cover Decision Problem

Instance: A graph $G=(V,E)$ and an integer $k$.

Question: Does $G$ have a vertex cover of size at most $k$?

Binary Programming Decision Problem

Instance: An integer $m \times n$ matrix $A$, an integer $m$-vector $b$, and an integer $l$.

Question: Is there a a 0-1 $n$-vector $x$ with at most $l$ 1's such that $Ax \geq b$?  Here $||x||_1= \sum_{i=1}^{n}x_i$.

I found a supposed transformation here that makes $A$ an $|E| \times |V|$ matrix, where $a_{e,v}=1$ if edge $e$ is incident on vertex $v$ and $0$ otherwise.  It also sets $b$ to an all 1's vector and $l=k$.

This transformation works in one direction: if you have a vertex cover you can build $x$ by letting $x_v=1$ if vertex $v$ is included in the vertex cover and $0$ otherwise.  However, in the other direction I can easily create an example where $Ax \geq b$ but the 1's in $x$ do not create a vertex cover in the induced graph.  Can anyone provide a hint as to how to correct this?
Your example does not hold since the first entry of $Ax$, 0 is smaller than 1, the first entry of $b$.

$$
\begin{array}{c c c}
&amp;Ax &amp;  &amp;b\\
&amp; \begin{bmatrix}0 \\1 \\2 \\1 \\1\end{bmatrix}
&amp; \not\ge\ 
&amp; \begin{bmatrix}1 \\1 \\1 \\1 \\1 \\\end{bmatrix}
\end{array}
$$

Please note the condition $Ax\ge b$ means every entry in $Ax$ is no less than the corresponding entry in $b$. In term of the corresponding problem, the vertex cover problem, it means every edge is incident to at least 1 vertex. It is not about the $L_1$ norm; otherwise, it should be written as, for example,  $||Ax||_1\ge ||b||_1$. 

Yes, we want to minimize the number of 1's in $x$, which is the same as minimizing $||x||_1$. However, the condition $Ax\ge b$ is a requirement on $x$. The requirements on the variable that are usually read as "subject to ..." and the objective function could be seen as irrelevant or independent to each other.