While I don't see a good reason to increased their prices and not mention it publicly, I'm definitely not against them raising their prices. Aside from the fact that it will add to Flippa's bottom line (which I'm sure was a healthy portion of the price increase), it also helps weed out the junk listings a bit.
If they make it more expensive to list sites that have a lower likelihood of selling, they'll keep more trash sites off Flippa I think. Additionally, they'll see a bump to their completely sales rate (I'm assuming) with a price increase up-front. I remember selling on eBay in what seems like another lifetime. I'd also listed on other "free to list" platforms that were absolutely HORRIBLE and filled with all kinds of junk. eBay was better because they charged up-front. (They continued to bump their fees, though, and ultimately I ended up feeling quite burned...that eBay was eating up all of my margins...something Flippa should carefully consider, I think)