The problem is that "$u(H)^\perp$ has finite dimension" does not imply "$u(H)$ has finite codimension".
"Codimension" is meant in the algebraic sense. For a (not necessarily closed) linear subspace $E \subset H$, "$E$ has finite codimension" means (among other equivalent definitions) "there exists a finite dimensional subspace $F \subset H$ such that for every $x \in H$, there exist unique $y \in E$, $z \in F$ such that $x=y+z$". In other words, $H = E \oplus F$ as a direct sum of vector spaces.
Let's consider the example I gave in my comment: $H = L^2((0,1))$ (it's simpler if we leave off the endpoints) and $u$ defined by $(uf)(x) = xf(x)$. Note that $u$ is injective since if $uf = 0$ we have $x f(x) = 0$ and hence $f(x) = 0$ for almost every $x \in (0,1)$. So $\ker u = 0$ which is finite dimensional.
It's easy to check that $u$ is self-adjoint, so we have $\ker u^* = \ker u = 0$ as well.
Also, we can see directly that $u(H)^\perp = 0$. Suppose $g \in u(H)^\perp$; then in particular $\langle ug, g \rangle = 0$. This says that $\int_0^1 x g(x)^2\,dx = 0$, so that $x g(x)^2 = 0$ and hence $g(x) = 0$ almost everywhere.
But $u(H)$ has infinite codimension. For $0 < p < 1/2$, let $f_p(x) = x^{-p}$. Note that $f_p \notin u(H)$ since if we had $u g_p = f_p$, we would have to have $g_p(x) = x^{-p-1}$ almost everywhere; but those functions are not in $L^2((0,1))$. Moreover, the uncountable set of functions $\{f_p\}$ is linearly independent. So if we let $F$ be the linear span of all the $\{f_p\}$, then $F$ has infinite (even uncountable) dimension and $u(H) \cap F = 0$; the codimension of $u(H)$ is infinite (even uncountable).
So for this operator $u$, we have that $\ker u$ and $\ker u^*$ are both finite dimensional (actually zero dimensional) but $u$ is not Fredholm.
Another way to think about the issue is that the orthogonal complement $E^\perp$ is not in general an algebraic complement of $E$; it's an algebraic complement of the closure of $E$. (You may be confused since in finite dimensions, $E^\perp$ is an algebraic complement of $E$; but in finite dimensions all linear subspaces are closed.) In particular, having $E^\perp = 0$ does not imply $E = H$; it only implies that $E$ is dense in $H$, but dense subspaces can still have large codimension.
As a final remark, it is not true in general that a linear subspace $E$ with finite codimension is closed (consider the kernel of a discontinuous linear functional, which has codimension 1). However, it is true in the special case that $E$ is the image of a continuous operator on a complete space.