Inertial coordinates only exist in special relativity, these are per definition those charts $(U, \varphi)$ such that
$$g := \operatorname{diag}(1, -1, -1, -1)$$
for all events $p \in U$, expressed using local coordinates $\varphi$. These charts are "declared" by virtue that the pseudometric must be $\operatorname{diag}(1, -1, -1, -1)$ in local coordinates. To what extent you are "choosing your inertial charts" or whether you "choose g" (or both simultaneously) is a mere philosophical difference.
In special relativity, inertial charts are related by the group elements of the reduced Poincaré group.
In general relativity, you only have inertial frames. There need not to be any inertial chart on a general spacetime $M$.
In general relativity (as opposed to special relativity), inertial frames are related by the group elements of the orthochronous Lorentz group (and the proper orthochronous Lorentz group if onwe wants to forbid orientation flipping).
The reason for why you can pretend that your chart is inertial in special relativity is that, in special relativity, you can identify the tangent space $TpM$ with points on the manifold. This is absolutely not true in general relativity and it is a grave sin to ever think of tangent vectors as embedded in the manifold. We often do this, because we are so indoctrinated by how it works in (affine) Euclidean space. In (affine) Euclidean space, we do not make any real difference between points and vectors.
The Euclidean plane, for example, can be thought as either:
a) all elements of a set $\mathbb R^2$ equipped with a vector space structure, or
b) the set of all two-dimensional "vectors" or "directions" anchored at some point deemed "the origin".
But this viewpoint breaks down on manifolds.
We have to remember that the manifold and its extra structure is merely a mathematical model for a real physical system. So we of course can, by our whim, define anything we want to mathematically. But the physically significant part is when we identify parts of that mathematical structure to real physical objects.
When we define our inertial charts (or our inertial frames, as in GR), we do so with a physical interpretation of what it means. We interpret an inertial chart $(U, \varphi)$ as "lines in $(U, \varphi)$ are geodesics with no acceleration". In general relativity, we interpret an inertial frame operationally as "a set of physical geometrical vectors that do not accelerate".
EDIT:
Someone mentioned the exponential map, and I think it is worth to explain what it is and the philosophical differences that I think are confused here.
The key point is that the exponential map is not determined by the smooth structure alone. The exponential map requires you to know what a “straight line” is, because that is how the map is defined: fix a point $p \in M$, and given a way to talk about “geodesics”, every tangent vector $v \in T_pM$ determines a geodesic $\gamma_v$ solving
$$\gamma_v(0) = p,\qquad \dot\gamma_v(0) = v.$$
Then define
$$\exp_p(v) := \gamma_v(1),$$
provided that the geodesic exists up to time $t=1$
So $\exp_p$ maps a neighborhood of $0 \in T_pM$ into $M$, and it sends the zero vector to $p$.
The exponential map essentially says:
- pick a direction and speed at $p$,
- follow the geodesic for unit time,
- land at a point of $M$.
This gives a precise way to replace $M$ by its tangent space near $p$, but only up to the first place where geodesics start to overlap or fail to stay minimizing.
On a smooth manifold alone there is no canonical exponential map. The construction is canonical only after you have fixed extra geometric data, and even then the exponential map can fail to be defined because multiple geodesics connecting the same points, or geodesics just “ceasing to exist”.
The main point is that talking about “straight lines” is fundamentally different than talking about velocities, and both are needed in order to do the whole “tangent space to manifold” identification thing. The differential structure and the projective structure are different independent specifications of data.
Neither is really more fundamental than the other, and even if you have both you can only do an “identification” in limited cases geodesics may cease to exist, or overlap). Thus, it is rather the proper way to never confuse the two, i.e. the manifold and the tangent space.
A sort of identification works in special relativity (and in Minkowski space, in particular) because geodesics never overlap and are defined by affine lines in an inertial chart. In Minkowski space (with a global chart), the exponential map is defined on all of $T_pM$ and is globally bijective.
In fact, the geodesics in special relativity are sort of defined very clumpsy and out of thin air, the only way to know if a curve is (locally) a geodesic is to start from a chart you know is inertial and check if the curve is an affine line there. In general relativity, one adds the proper projective structure to talk about acceleration, in which charts does not matter again (as they “should not” do).
The cleanest chart-free version in special relativity is to use the fact that Minkowski spacetime is not just a manifold, but an an affine space with a translation-invariant Minkowski metric. That affine structure gives a canonical way to compare vectors at different points, so you can define acceleration without choosing coordinates. But the point is that one still has to "choose the inertial charts" (what charts counts as "inertial"). If one says "no inertial charts" and then immediately writes things $\nabla_u u$, one has only moved the machinery around. In special relativity, the connection is usually not "an extra physical structure" in the way it is in general relativity.