I had this same problem, but for $90 its easily fixed 🙂
First off, if you have MTS files, I assume you are using AVCHD cameras? If thats the case, when you grab the data files from the SD Card or whatever media you are recording to, it is critical that you grab the entire directory structure. From there, you can use File->Log and Transfer and select the base directory, and Final Cut Pro will import everything for you.
However, if you made the same mistake I did and only saved the MTS files, you can not import them directly into Final Cut Pro. There are two worthy options though, and both will product MOV files of the same quality as if you grabbed them from FCP Log and Transfer. First is VoltaicHD. This runs about $30, but its very slow. It takes about 12 minutes to convert every 1 minute of footage, and occasionally it bombs out. The better solution is to buy Toast 9 from Roxio ($90 I think). From in Toast, go to the convert tab, drag your files in, and go to town. Toast is a pretty quick conversion in comparison to VoltaicHD.
Keep in mind your output files from FCP, VoltaicHD, or Toast will be interlaced, but you can deinterlace in FCP for web output or let FCP select the correct output for DVD or other media.