Orientation of Polarized Capacitor in a High Pass Filter
Short answer
There's a mistake.
Details
Normally, you want an electrolytic capacitor's positive terminal to be connected to a node having greater voltage.
In the given schematic, most likely the highpass filter formed by 1000μF-1kΩ pair is there to remove just the DC offset along with very low frequencies because its cutoff frequency is around 1.6 Hz. So, since the input signal is a 5V PWM with variable duty-cycle, the expected output is an AC signal with positive (+2.5V) and negative (-2.5V) peaks: The input has a 5V peak, and the output will have a 2.5V peak (max.)1. So the positive terminal of C1 should be connected to Arduino's output.
1 There's the transistor with its emitter connected to the speaker, so the output will not have equal-amplitude peaks actually. This will not change the conclusion, though. You can simulate the circuit. By the way, I have no idea why the load is connected to the transistor as shown.