Because some ISPs are trying to maximize their revenue by charging Netflix directly.
There are a few other legitimate reasons as well. Some ISPs dislike hosting hardware that they don't own in their data centre. Or it may be that an ISP has contracts in place that commit the ISP to certain bandwidth costs, so removing Netflix traffic may not actually save them money.
Why shouldn't an ISP charge Netflix to host a box in their datacenter? I'd charge you a fee if you wanted to store your DVDs in my house, even if you let me watch them.
On the other hand, if the ISP also runs a video service, they've got some very compelling reasons to do everything they can to not increase the quality of service for Netflix. They're green, and rectangular, and...
There are a few other legitimate reasons as well. Some ISPs dislike hosting hardware that they don't own in their data centre. Or it may be that an ISP has contracts in place that commit the ISP to certain bandwidth costs, so removing Netflix traffic may not actually save them money.