Not technically (I think) a limitation of the new Fusion Drive per-se, but more a limitation of the drive size and it's interaction with the BootCamp drivers. Either way, if you got yourself a shiny new iMac with a 3TB fusion drive and found you can't install Windows, you'll want to check out Installing Windows via Boot Camp on a 2.2 TB or larger Drive in Lion and later over on TwoCanoes.com.
Boot Camp Assistant is not supported by Apple for hard drives larger than 2.2 TB. If you purchased a new iMac with the 3TB option (either with a Fusion drive or just a standard drive), Boot Camp Assistant will refuse to partition your hard drive into a Mac and Windows partition. However, it is still possible to create a working Boot Camp partition for Windows, provided you use the partitioning scheme as outlined in this tutorial.