1) When your Windows is infected by boot sector virus or the like, it will corrupt your partition table, there is no difference whether you are using NT/BSD bootloader. This makes your FreeBSD an innocent victim. That's why many FreeBSD dualbooters often ask "why my machine suddenly refuses to boot up?"
2) Interruption and inconsistency:
- Your mom: Hey, why can't I send mail?
- You: sorry mom, I am not using FreeBSD at this moment
- Your buddy: Hey, I haven't finished downloading the 600MB ISO file from your FTP server. Why you reboot to Windows?
- You: Sorry I don't boot into FreeBSD all the time.
- Your buddy: WTF.
You might argue that you don't use FreeBSD as a server OS. If that's the case, why bother to try FreeBSD in the first place?
3) Extended caution:
Since you are new at this, you need to invest more time on learning the OS. As a beginner, you will often end up reinstalling the OS over and over again if something isn't done right. When reinstalling or upgrading, if you have done something incorrectly, both Windows and FreeBSD can fsck'ed up, even they are on a different disk, not to mention if they are on the same physical disk.
4) Different OS, different configuration. It's a waste of time to sync your bookmark, preference, addressbook, ICQ contact lists or the like when you are booting into one or the other. Well, you might say you can store them in your Windows partition and mount them while using FreeBSD. Look at (1) above. In addition, things just don't work well when you are relying on some files that reside on msdos partition while you are working with FreeBSD. When FreeBSD crashes, it's possible to damage your msdos partition causing you unable to boot back to Windows any longer, or lost of data at the very least.
5) Hardware is no longer unaffordable. If you can't even afford to buy a McDonald mini-meal, FreeBSD is not your toy. Unlike Windows, FreeBSD runs okay on 486 with 16mb RAM and 2GB hard disk. Why can't you build another box and avoid all the troubles?
In the end, I have to say FreeBSD needs consistency. So STAY UPTIME! DON'T REBOOT!. Booting into Windows today then boot into FreeBSD tomorrow is just inconsistent.