I have updated both of my iPads (original and the 3rd generation) every time that an update was available - on the day that the update was available. I have never had a problem that was caused by any software update.
There will always be people reporting failures and problems with updates. Sometimes things happen. Sometimes It is not the update itself, but maybe an interruption in the Internet connection (using WiFi to update), a problem with iTunes on the computer, a problem with the computer itself (using iTunes to update).
The overwhelming majority of users experience no problems at all with the software updates and I would never hesitate to update my iPad when another update is released. You must make the choice on your own. If you aren't comfortable with the update, don't do it. I think, though, that you just had one of those fluke experiences and odds are it will not happen again.