My understanding is that an arbitrary quantum-mechanical wavefunction can be written as a linear combination of eigenfunctions of some Hermitian operator, most commonly the Hamiltonian; when a measurement corresponding to that operator is made on this superposition state, the wavefunction collapses and only specific values are observed -- namely, the eigenvalues of the particular eigenstates that comprised the wavefunction. (Moreover, the probability of measuring the eigenvalue $E_i$ is proportional to ${\|c_i\|}^2$, the square of the coefficient of that eigenstate in the linear combination, etc.)
And yet, in many situations, it seems to be assumed that the system is already in an eigenstate and that superposition is not possible. For example:
the electron in the hydrogen atom is said to be in, e.g., the 1s $^{2}S_{1/2}$ state or the 2s $^{2}S_{1/2}$ state, but never a superposition of the two.
the possible angular momentum vectors for a QM rigid rotor with fixed $l$ are sometimes drawn as discrete "cones"... but couldn't the average $\bf{L}$ point in any direction, since a rigid rotor might be in a superposition of states?
when deriving Boltzmann statistics, we consider how to place $N_i$ particles into the level with energy $\epsilon_i$, but there is no consideration that a particle might occupy two (or more) energy levels simultaneously.
Why do we ignore superposition in these and similar cases?