To make a long story short, (I go into more detail about how and why in my book
) they just don't do a great job at what they are supposed to do.
Now - don't get me wrong - having something measure your tempo is really really important. I just don't think the metronome is the best tool for the job. Instead, I advocate using a step sequencer, such as a drum machine. There are many free phone and browser apps, as well as more fully functioning programs such as Fruity Loops where you can program in something that is a bit easier and FAR, FAR, FAR more pleasant to work with.
Step sequencers allow you to craft repeating patterns that can specifically support you and what you want to practice. You can delete bars, and do a lot of other things that most metronomes don't allow you to.
It is possible to enjoy the click of the metronome - I do. At least now I do. I suffered through the click for years before I learned to enjoy it. The cold, non musical click just drove me batty. Instead use a drum machine to create something that is fun to play along with. You'll get more out of your practice time and have more fun to boot. Why make things harder on yourself?