Yes, the chassis is ground, but the bias supply is providing a negative voltage to the grids of the power tubes to keep them biased. Since all the voltages involved along the bias rail are lower than ground (negative), you must keep the positive end of the caps on the high side (ground) and the negative end of the caps on the bias rail.
The - designation on the cap doesn't automatically mean that end always goes to ground. It just means that end must be at a lower voltage potential than the end marked +. We're so accustomed to working on circuits where all the voltages are above ground, we assume the - end of the cap is always towards ground.