First of course you'll have to get from San Pedro to Belize City. The boat will be US$12.50 a person, and if you fly into Municipal (about half the cost of flying into International) the price is about US$26 one-way.
From there you have several options. The cheapest is the bus. Batty's and Novelo's run frequently (they each have a station -- you can take a taxi for a few dollars from municipal) -- it's about 2 1/2 hours and about US$3. Price varies slightly depending on whether you take a local or express bus and might be a little more for destinations on the west side of San Ignacio, as Windy Hill is. Nice trip, and Windy Hill is right beside the highway, so the bus will drop you.
You can also take a van (duPlooy's, Venus, Aguada and others run them about once a day, for US$25 a person.)
Windy Hill's option obviously would be the easiest but by far the most expensive.
As to renting a car, it's easy and safe, though not cheap. Figure at least US$65 a day. It can save you lots of money, though, as you won't have to pay high fees for tours. I recommend Budget, but Avis I think is the only rental place with a regular location at muncipal, though any of the renters will deliver a car to you there or pick you up and take you to their office.
Windy Hill is for sale, I'm told, but it appears to be operating normally.
Belize First Magazine http://www.turq.com/belizefirst/