Note that the number of reflexive relations is $2^{n^2-n}$.
By definition, a binary relation ~ over a set $X$ is reflexive if for all $x \in X$, we have $x$ ~ $x$.
The example give below should clear your doubt on which relations are reflexive.
Let $X=\{1,2,3,4\}$ and define binary relations $R_1,R_2$ and $R_3$ on $X$ as follows:-
$R_1=\{(1,1),(2,2),(3,3),(4,4)\}$
$R_2=\{(1,1),(2,2),(3,3),(4,4),(1,4),(2,3)\}$
$R_3=\{(1,1),(2,2),(4,4),(1,4),(2,3)\}$
Note that $R_1$ and $R_2$ are both reflexive by definition.
But $R_3$ is not reflexive since $(3,3) \notin R_3$.
From this example for your relation matrix, we observe the following:-
$(1)$ A reflexive relation may contain elements which are not on the diagonal in relation matrix.
$(2)$ If a relation does not contain a diagonal element in the relation matrix, then it can't be reflexive.
With these two facts, it is easy to calculate the number of reflexive relations.
Sketch: Fix all the diagonal entries in the $n \times n$ relation matrix. For the remaining $n^2 – n$ entries, choose whether to put the elements corresponding to these entries in your relation. In the end, the relations obtained are reflexive by definition and there are $2^{n^2-n}$ of them.