There are plenty of good hotels in the $50 price range – Crown Regency, Citi Park, Alpa City, Quest, Eden, just to name a few. They all come with free wifi, A/C, hot/cold water etc, etc,.
When I was in Cebu, I stayed at the Castle Peak Hotel for 2 nights before heading to Bohol. The rate then was $35/night – A/C, wifi and the likes were included. We did a walk-in booking & the price we paid was much lower than if we were to book from outside the PI.
http://www.castlepeakhotel.net/ Whatever hotel you choose, only book for a day or two. If you like the place, then you can extend, if you don’t like then you can easily get another hotel.
I never encountered hot towel surcharge, towel deposit, pay extra for A/C or A/C limit or the likes. But, if you get a super cheap hotel, then yes you may encounter these charges - you get what you pay for.
FYI, I would not recommend these super cheap hotel.
Also get & keep receipts for everything - hotels, tours, shopping, etc,. You may need them later for evidence.