I've had the same thing happen too. It is scary but most of the times if is lack of experience more than a fault of the boat.
That said, here is a movie clip that I saved from a couple of years ago, mostly as a lesson to myself. We were out in Buzzards Bay and coming out of a no wake zone I started to pass another boat as I have done many times before. You can just see the wake ahead of me in some parts of the movie. It wan't an exceptionally large wake but at around 6 seconds I cross the first wake no problem (despite the Admiral saying "Oh-oh"), at around 25 seconds I cross a second wave no problem but you can hear the RPM's come up as I start running down the back side, and at 35 seconds I cross a third wave and you can hear a slap as we land. Then on the last wave at 40 seconds the prop catches a little air and breaks free a bit and the RPM's go up noticably, I chicken out and cut the throttle which causes the baot to roll in the trough and scare the crew. If I had kept the power on the boat would have punched through okay. Lack of skill and confidence on my part. Here is the clip (10megs):
Chicken Out
Like Willy said test and practice under controlled conditions to become familiar with how your boat behaves and learn its capabilities and limitations. Crossing wakes is very much like running in a following see so if you learn how to handle wakes well you will be learning a valuable skill that may come in handy under more severe conditions. Later that day we practiced in some standing waves at the entrance to the Cape Cod canal.