Most bots target the game's "Casual" mode, since it's the easiest way to hassle the largest group of people. If you play that mode, you will encounter bots. It sucks that you have to curate your own experience, but you can almost entirely avoid the problem by choosing your own community servers to play on instead.

IMHO: I'd argue that community servers are a "purer" TF2 experience in the first place. So many core game features only make sense in a pro-social "hangout" environment. I'll rattle off a few from the top of my head:

• Super long map timers are enjoyable as long as players can leave/join at any time
• Unrestricted joining/leaving/teamswitching works as long as autobalance and votescramble exist
• votekick/votescramble are great as long as people aren't encouraged to abuse the system to gain an edge

Casual rips almost all of that out in favor of emphasizing the gameplay skeleton which remains. You're no longer showing up to a permanent place with people you can get to know and be silly with. When the round timer ends, Valve may as well be blowing up the server and nervegassing the other 23 players for all it affects you. I posit that TF2's Casual mode isn't merely a "non-competitive mode" -- it's an "anti-social mode". Playing TF2's Casual mode is like... showing up to the amusement park, alone, except all of the restaurants and bathrooms are permanently closed and they lock the exit gates behind you.

For the most part, yeah. The only way to avoid getting into matches with bots is to find community servers with active moderation. I queue into Uncle Dane's servers when I feel like booting up TF2.