No, or at least the canonical bijection is typically not an isometry. For instance, let $X=\mathbb{R}^2$ with the Euclidean norm, let $F$ be the span of $(1,1)$, and let $Y$ be the span of $(1,0)$. Then $F\cap Y=0$, so $\frac{F}{F\cap Y}=F$. But the canonical bijection sends the element $(1,1)\in F$ to the coset $(1,1)+Y=(0,1)+Y$ in $\frac{F+Y}{Y}$, and $\|(1,1)\|=\sqrt{2}$ but $\|(0,1)+Y\|=1$.
(In this example, $\frac{F}{F\cap Y}$ and $\frac{F+Y}{Y}$ happen to be isometrically isomorphic, but not by the natural map. Probably you can get a similar example where they are not isometrically isomorphic by any map (say, take a similar example where the quotient spaces end up being 2-dimensional and you have a less symmetrical norm than the Euclidean norm), but proving that no map can be an isometry is probably kind of a mess.)
However, the canonical bijection is always an isomorphism of topological vector spaces. Indeed, the canonical bijection is norm-decreasing as a map $\frac{F}{F\cap Y}\to\frac{F+Y}{Y}$, since given $f\in F$, the distance from $f$ to $F\cap Y$ cannot be smaller than the distance from $f$ to $Y$. So the canonical bijection is a bounded linear bijection $\frac{F}{F\cap Y}\to\frac{F+Y}{Y}$, which is hence a topological isomorphism by the open mapping theorem.