Not sure how it is in other states but here in Maryland during the primaries I was surprised that it was no longer computer voting and had returned to a paper ballot
Voting is controlled by each state; not that you can't put forth the effort to manipulate votes in a certain state (ahem, Florida), but it would take a massive (huge) operation to work through this on even a single state level, much less a national election. According to
this, there were 5,400+ polling places in Florida alone (in 2004). If each polling place has 5 machines (just a guess), we're over 27,000 machines to manipulate. It seems it would be difficult to manipulate this centrally since each polling place reports results directly, so you'd have to touch each of the 27,000 machines to affect an election. Seems like you'd know if this sort of thing were happening, unless you're the sort that really enjoys Dan Brown movies.