The fear is that Apple might want to jack its new A series of ARM processors in future MacBooks.
There would be a lot of advantages for Apple if it could replace Intel chips in Macbooks with something home grown.
Apple is all about control and this would give it control over product release schedules and its intellectual property - it wouldn't need to compete with competitors for its supply of processors and would have more flexibility to fine-tune the battery and overall performance.
However it would be a move away from what Apple has done very well. Basically take an off the shelf Intel rig, stick it in a snappy looking case and make sure it works with OS-X. Apple really would be creating an innovative product, and it is a moot point if it can be bothered when the PC market seems to be dying and it makes most of its cash off mobile toys.
Apple certainly has the people in place to pull off a stunt like this. It has bought chip makers such as Intrinsity and PA Semi and built several A-series chips. An A6 chip expected to power the iPad 3 in early 2012 has just entered trial production, though no details on its design have yet to surface.
The fact that Intel is worried is probably an indication that it will have some work to do to keep Apple as a customer rather than a rival.