It's just an unfamiliar representation: with the secondary dot-phasing and diode direction as shown, the output and input have opposite polarities. The winding phase and diode are usually reversed so the input and output polarities are the same. That's just a convenience; it's not necessary in order to make the circuit work. Assume the supply polarity is positive at the top. During the Don interval, the supply can force current into the primary because the switch is on. That means the positive end of the primary is its dot end. Therefore the secondary's dot end is also positive, so the diode is reverse-biased and stays off. During the Doff interval the primary is no longer sinking current, because the switch is off. Being an inductor though, it still tries to keep current flowing through itself in the same direction as before. It can only do that by trying to force current through the circuit, so its polarity must reverse: its positive end becomes the non-dot end. The secondary therefore also becomes positive at its non-dot end. That forward-biases the diode, which turns on and delivers current to the capacitor and load - with the output positive at the bottom and negative at the top, opposite to the supply's polarity.