You can still print out labels through PayPal and get the commercial rate, just not through USPS directly.
Basically when the price went up from 5.25 to 6.80, it was a combo of two factors. The rate itself going up over 10%, and USPS no longer offering people the commercial rate when printing through their website.
Can't do anything about the rate going up over 10%, but you can still get the commercial rate by using this link and paying for the label with PayPal. Using this method, a small flat rate box is 6.10 (instead of 6.80) and a medium flat rate is 11.95 (instead of 13.45).