No, $\{\langle D,M\rangle\mid D\text{ is a DFA }\land M\text{ is a Turing Machine }\land L(D)\subseteq L(M)\}$ is not recursively enumerable.
Let $Z=\{0^{n}\mid n\ge0\}$. Call a Turing Machine (TM) $M$ a $Z$-TM if $Z\subseteq L(M)$.
Claim. $\{\langle M\rangle\mid M\text{ is a } Z\text{-TM}\}$ is not recursively enumerable.
Proof (by diagonalization): Towards a contradiction suppose $\{\langle M\rangle\mid M\text{ is a } Z\text{-TM}\}$ is recursively enumerable. That implies there is Turing machine $A$ that enumerates all $Z$-TMs, i.e., given a natural number $n$ as input, $A$ will output (the encoding of ) a $Z$-TM, which is denoted by $C_n$ such that the set of all $C_n$ is the set of all $Z$-TMs.
Let us construct TM $B$ so that on input $w$, $B$ will check first whether $w$ contains only $0$s.
- If not, $B$ accepts. (The behavior of $B$ here does not matter.)
- If yes, $B$ computes $n$, the number of $0$s in $w$. Then $B$ will use $A$ to obtain $C_n$. Then $B$ will simulate $C_n$ on input $0^n$, until $C_n$ accepts. Then $B$ will run one more step and accepts.
$B$ is different from each $C_n$ for all $n$, but $Z\subseteq L(B)$. This means $A$ misses $B$ in its enumeration of all $Z$-TMs. $\quad\checkmark$
If we can enumerate all pairs of $D$ and $M$ such that $L(D)\subseteq L(M)$, we can further select the pairs such that $L(D)=Z$, since it is decidable whether $L(D)=Z$. Then we can enumerate $Z$-TMs. This contradicts the claim above.