I don't believe that online poker is rigged in any way. The computer programs that determine which cards to deal are every bit as random as a thoroughly shuffled physical deck of cards. But there are several factors that make some people believe the system is "rigged" or skewed in some way.
#1: Hand speed. Online poker moves much faster than live poker. Players typically have a strict time limit to make their play, players can declare their move before their turn an the computer acts instantly when it becomes their turn, and the computer can award chips to the winner then shuffle and deal the next hand in a split second. As a result you will usually see at least 5x more hands per hour online than in live poker with ratios even higher at times. When you play more hands, you are going to see more "unique" or memorable odditites like bad beats, monster hands, long shot draws etc. These things WILL happen and the more hands you play the more of them you'll see.
#2: Multi-table play: Its common for players who take online poker seriously to play more than one table at a time (through split screen or multi-monitor set ups, or sometimes even multiple computers). This just compounds issue #1 by further multiplying the number of hands per hour you can see and drastically increasing the frequency of those memorable oddball hands.
#3: Lousy players: In free roll or low limit online poker you will find a lot more terrible players, for example players who will call with nearly any hand pre-flop (and opponents who will let those lousy players get to the flop without a raise). As a result you have more players drawing and more odds that someone will hit something, so you see a lot more bad beats & crazy draws because you aren't starting every hand by eliminating players with low cards.
#4: Calling stations. In addition to bad pre-flop play you have a lot of "calling station" players who just call every bet all the way to the showdown. So you see more of the late draws or mediocre hands being beaten where better players would have folded earlier, before you saw their hand (and before the bet half their stack on a gut shot draw).
I think that if you took the time to take long term data (at least 1,000 hands, preferably much more), and analyzed the results of online poker vs live poker you'd find there isn't much difference in results, and the differences you do find would be attributable to player decision making, not to rigged decks