Where does the negative sign come from in this transfer function?
The output signal: \$\quad y = d-C(s)M(s)e\$

The error signal: \$\quad e = r-y\$

$$
y = d-C(s)M(s)[r-y]
$$
$$
(1-C(s)M(s))y = d-C(s)M(s)r
$$
From superposition principles, take \$d\$ as 0 and you get the transfer function from \$r\$ to \$y\$:
$$
y = \frac{-C(s)M(s)}{1-C(s)M(s)}r
$$

As can be seen, the minus sign comes from the first equation. If you were to redefine \$y = d+C(s)M(s)e\$, then the following equation would hold:
$$
y = \frac{C(s)M(s)}{1+C(s)M(s)}r
$$