Even though I'm a 49ers fan, I'm a big fan of Zach Miller. I grabbed him as a rookie in a fantasy football dynasty league I used to be in and have been a fan of his ever since. And it looks like he's really stepped up his game for the Raiders in 2010. Part of that might have to do with the issues surrounding the Raiders WR talent, but there's no doubting that Zach Miller is a very solid tight end.
The 49ers have indeed done a solid job covering tight ends. I'd look at a couple of reasons for that. Manny Lawson has been a bit inconsistent in his pass rushing skills, but in coverage he is strong. The 49ers often use him to cover the opposing team's tight end, particularly when dealing with a big time talent at the position. Accordingly, I'd expect Lawson and Miller will be battling for much of the afternoon.
The 49ers have also utilized Parys Haralson and Ahmad Brooks in coverage, and while each can be solid at times, I trust them a lot less than Lawson. And even 49ers all-world linebacker Patrick Willis is developing his coverage skills. He's known as a ferocious tackling machine, but he's worked hard to improve his coverage skills.
The other lesser reason teams might not be going to their tight ends as much is because of the 49ers struggles against receiving running backs. As was mentioned earlier this week, the 49ers rank dead last in DVOA when it comes to covering running backs in the passing game. It's entirely possible teams don't feel the need to go to the tight end if the running backs will eat the 49ers alive.