One of the main reasons people bot is to level their character up to a certain level quickly, skipping over content they've already done. This is against the rules according to Blizzard's terms of service, there's no question about that, but morally and pragmatically speaking for some individuals, it's not outside the bounds of acceptable behavior. People's reasoning is that if they've already done the content – why should they be forced to repeat it? This is a valid criticism of the game, no matter if you support botting or not. And within that valid criticism people have came up with a solution – botting.
A primary negative effect that is often cited as a reason to not allow characters to level via bots is that it devalues the meaning of a max level character. While this might be true when looking at the system with quantitative measurements (ie: everyone has a 70 of every class), it is not true on the qualitative side. A person that has leveled his or her character to 70 by hand will have a much better grasp on the fundamentals of the class than a person who had botted his or her way to 70. This is a key point: the botter is going to have problems playing the game at 70, while the non-botter will naturally transition into the end game. Eventually few people will want to play with the botted character, and thus by natural laissez-faire principles, the botters will have less incentive to bot over leveling a character the normal way – thus correcting the problem itself. If anything, the botter is only cheating himself out of the leveling experience, not affecting the rest of the WoW community.
Another key reason people bot is because of the economic value to them. If they can set their bot up correctly they can bring in hundreds of gold an hour – all automated. This frees the botter up to do other things in life. Positives of this include the ability to collect the large necessary quantities of materials often required of high end profession leveling, and the ease of making money off of other items collected.
An often quoted negative of botting for economic reasons is the impact on the in-game economy. While it is true that botters have a tendency to create "wacky" situations in the economy – it is also true that a non-botter can. For instance, say a botter uses his botting-enhanced farming to pick up hundreds of high level enchanting mats. He then goes on to sell them all on the auction house. Because his artificially created supply outweighs the demand by so much, the price of the materials plummets. This is not a good situation for those trying to make money, but at the same time it is a good situation for those needing the materials.
At the same time a non-botter can cause just as much economic turmoil in the economy. Take something that I've been doing lately. I have a product I'm selling on the AH, we'll just call it Super Widgets for the sake of discussion. These Super Widgets have a normal economic value of 1000g. However there is limited demand for these Super Widgets, and I have (by normal non-botting means) obtained a large supply of the Super Widgets. I want to create a natural looking economic situation where the price for Super Widgets goes up. What can I do? I set several Super Widgets high above normal market value – say 4000g. I leave these up at that price indefinitely. On another alt, I sell a few more Super Widgets for 2000g, and then a couple on another alt at 1500g. Each price level is done on a different alt, so it appears as if there is a price war going on for my Super Widgets amongst many people. Unsuspecting individuals will see the Super Widgets for 1500g, buy them, and enjoy them with the false knowledge that they've beaten a high end price by 2500g. However they've actually played into my hands by 500g, giving me some nice profit on an item I have large quantities of. In addition to creating artificial pricing situations, I have more or less created an artificial demand for these Super Widgets. Nothing is more destructive to an economy than artificially created supply and demand situations. To sum up my point and be very clear: a player can have just as destructive a force via normal (and legitimate) means as a botter can have via abnormal (and illegitimate) means.
Perhaps the most hotly contested of the reasons people bot is because of the PvP system. It is possible for bots to earn honor and rewards via gear and other such token turn ins faster than a non botter. A typical (smart) botter might go smack a few players around in a battleground, and then leave the rest of the game up to the bot. This will have the effect of giving him the rest of the honor and token from the game with only a fraction of the work of others. More so, this action is repeatable easily throughout an entire day with barely any effort on the part of the botter.
Obviously, this can throw off PvP gear balance if done on a massive scale. However, does it really? These botters will still suffer from the lack of PvP skills as they haven't worked on their abilities through countless battles. While they may have more gear than some people, their PvP skills will be lacking and cannot be made up for. Again, it appears the botter is "cheating" only himself out of his skill, and not the rest of the greater WoW community.
In conclusion, it is rather clear to me that while botting in WoW is against the terms of service (and I highly advise everyone not the break them), it is not against the greater WoW community's good. Botting just doesn't have any adverse effect on a large number of people, and any effect it does have isn't any more than can be done by a person playing the market or battlegrounds in a particular way.
While it is definitely within Blizzard's right to remove the botters because of the terms of service, one has to wonder if this is the best action. In my opinion, it is not. Let them play the game the way they want, and I'll play it the way I want. Since they don't affect me anymore then any other person in the game does/can I don't really care; and that answers my original question. Do botters really matter? No more than we let them.
For those wondering, the picture for this article is of D'Anna from Battlestar Galactica. While she looks human, underneath her skin she is nothing more than a conflicted (ro)bot.