I have never had a problem with this. Not as a runner, not as a biker. I sometimes get upset with the equestrians, but most runners and bikers are polite enough to not crap in the middle of a trail, so my main gripe with horses doesn't really apply to them. As corvuscorvax said, bikers are supposed to yield to pedestrians, and both are supposed to yield to equestrians. As a biker, I yield...it doesn't really interrupt my flow. As a runner, 99% of the time, bikers are respectful enough to yield to me, though if they're in the middle of a rock garden or something, I'll get out of their way (though before I started biking, I wouldn't have even thought to do that, not because I was feeling superior to them, but because I honestly wouldn't have realized it would be a problem). If I'm on my bike and really don't feel like dealing with runners, I go to the BMX track. If I'm running a tempo run, I go somewhere with no bikers. Also, you DON'T RIDE OFF THE TRAIL AND INTO THE WOODS TO AVOID PEDESTRIANS AND EQUESTRIANS! Get to the side of a trail and either put a foot down or wait for 5 seconds. It's not that hard.

Have you asked the runners to help maintain the trails? And I don't just mean grab them on a trail and make some smartass remark to them because that's just going to strain runner-biker relations and breed hostility. I mean honestly reach out to them about trail maintenance days. I've known a lot of trail runners who do every bit as much trail work as mountain bikers. I've actually done way more work on trails with fellow runners than fellow mountain bikers. If they didn't build the trails, they don't know when to work on them (and trust me, you don't want them working on them without you either, since the ones who don't mountain bike don't realize that jumps and other features are there for a reason, and honestly think that someone just didn't clear out that part of the trail).

That said, any "runner" who's running on a trail with actual jumps (as opposed to features that you can get air off of or there isn't an alternate way down) is a stupid jolly jogger who clearly isn't getting a very good workout, since it's kind of impossible to run on dirt jumps. Just saying.