Here are some of my lures with hook bonnets on them:
What if a lure has a treble hook AND one of those hooks on top that also gets caught on everything? Most of those types of lures come with the answer to that question. Look at this picture:
Here is what one of my spinner boxes looks like:
The only problem I have with hook bonnets is sometimes remembering to put them back on. Some days when I empty my pockets after a day at the lake I pull out 2 or 3 bonnets from my pocket. If I can remember all the lures I used that day, it's pretty easy to find the naked hooks, otherwise I pretend it was time to go through and organize all my lures anyway.