Robert, I think this is a question that has been at the top of the list for many players for a while, and is fast rising to the top of the list for other players too.  I don't know that I can answer your question fully as I'm not sure I have all the information myself, but here goes:

The protection you need is from sophisticated robots that are not known or understood generally, so how many of them are out there and what they are capable of, no-one knows.  I make this distinction from the "$49.99" robots you see advertised.  Without even looking at them, I can confidently predict these are worse than useless and any purchasers have wasted their money, which is what they deserve.

So, the concern is largely over the unknown.  Some may me making millions using them; on the other hand maybe no one has yet.  It is a fair bet to say though that a lot of people will certainly be trying.  So, what are the poker sites doing?  Unfortunately their standard line is "they have sophisticated anti-bot measures and actively monitor their games for possible bot play."  However, they won't go into any detail on the grounds that it would make it easier for the cheats to take it to the next level.  So, your guess is as good as mine as to how effective they have been.  Perhaps they could publish their results on this at least. I have never seen a report of any such instances caught by a poker site, I guess they want to hide the naughty stuff and try and present a whiter than white environment.

So, to answer your question directly, you can't protect yourself, I think you have to place a degree of trust in the site that you choose to play at, so choose a reputable site and support any site that takes the lead with anti-corruption measures.  Otherwise in a few years you could sit down with a player that is using 3 accounts at your table, 3 other players that are openly colluding and soft playing each other, and 3 players that are actually robots, of varying quality.  Talk about game selection! The reality may well be that if the sites don't sort it out in the next year or two, online poker could well struggle.