bmatrix: how to align elements' subscripts?

To align the 4 terms on their subscripts, I suggest you combine a bmatrix*[r] environment (provided by the mathtools package) with a \mathrlap{-} instruction (also provided by the mathtools package).

Update: to perform vertical alignment of the k subscripts in the first row, I suggest you provide add a \vphantom{-} superscript term to \mathbf{C}_k term in the upper-right cell.

The result of the adjustments is shown in the lower matrix:

\documentclass{article}
\usepackage{mathtools} % for bmatrix* env. and \mathrlap macro
\begin{document}
\[
\begin{bmatrix}
\mathbf{P}^{-}_{k} & \mathbf{C}_k \\
\mathbf{C}_k       & \mathbf{S}_k
\end{bmatrix}
\]

\[
\begin{bmatrix*}[r]
\mathbf{P}^{\mathrlap{-}}_{k} & \mathbf{C}^{\vphantom{-}}_k \\
\mathbf{C}_k                  & \mathbf{S}_k
\end{bmatrix*}
\]
\end{document}

Here are two possibilities:

\documentclass{article}
\usepackage{amsmath}

\begin{document}
\[
  \begin{bmatrix}
    \mathbf{P}^{-}_{k} & \mathbf{C}^{\vphantom{-}}_k\\
    \mathbf{C}_k & \mathbf{S}_k
  \end{bmatrix}
  \begin{bmatrix}
    \mathbf{P}_{k}\llap{${}^{-}\mkern -3mu$} & \mathbf{C}_k\\
    \mathbf{C}_k & \mathbf{S}_k
  \end{bmatrix}
\]
\end{document}

Note: the second method uses manual adjustment for the horizontal position of the minus exponent (see the \mkern -3mu).