My daughter was scared for a time of ants (about the age of 3 and turning 4) and many other bugs. Ignorance is the beginning of fear. I caught ants and bugs in one of those bug boxes that the kids can look at. Explained that the bugs couldn't get out. I also caught harmless bugs and let them crawl over my hands. Ladybugs, Daddylonglegs, Ants, caterpillars and other things that didn't bite or hurt. When she saw that I didn't have fear of them she began to be curious. Kids will mirror your feelings about things so if you're afraid they'll probably be afraid. My daughter is VERY curious about bugs now and I've had quite a few jars of bugs brought into my home. Not to mention a cup full of ants one time released on my kitchen counter.
Just take every opportunity to show him that some bugs are harmless. Just make sure that you teach him to respect bees. My daughter tried to catch a dying bee once without knowing the stinger was there. I got her a magnifying lens and showed her the stinger. We talked about how they might get scared if you try to catch them and that's how they protect themselves.
Get books about bugs and talk about how they help you with things. Spiders eat mosquitos. Ladybugs protect your plants. Flies clean up garbage. Things like that that show the value of bugs. The more he learns the less he'll be afraid.
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"Always learn the rules so that you can break them properly." Dalai Lama
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