It's an instinct shaped by many thousands of years of people scared of spiders (and snakes, tigers, dark places, huge cliffs, etc.) having a slightly better chance of surviving and mating. Many of these dangers aren't really dangers anymore to civilized humans, but ancient instincts don't know that.
I personally don't like spiders at all, and I live in an old house with lots of them in the backdoor/kitchen area. I try to live in peace with them and just kick them out, but occasionally it gets too much and I kill one. Need to get better about this. I agree that killing anything without a need is...well unnecessary. Not their fault they are so incredibly ugly.
You're right, fear is a necessary instinct, or else we'd be killing ourselves left and right by hugging bears and playing catch on the freeway.
As long as you don't kill things needlessly, than you have my respect. (Personally, I find spiders pretty darn beautiful, lol! That's coming from someone with a 8" spider living next to his bed though)
A good example of the opposite is my neighbor that moved in recently. I have chickens, and with chicken feed comes pests. Lots and lots of rats. Eventually I started getting snakes, big 6' black rat snakes. At first I was a little apprehensive about these formidable creatures sharing a yard with my feathered friends, but it was apparent they were there for the rodents, after one morning I happened across one in the process of eating a MASSIVE rat. I accidently scared it off from it's meal and I got a chance to weigh the rat, it was 2 1/4 pounds! The snakes grew really tame after coming across them many times a month, and I eventually could tell the difference between the two different and constant visitors. After having them stick around for nearly 3 years they both had names and the bigger of the two, jokingly named Big Black Bertha by my friend, measured a total of 91 inches - close to the record! Both were tame, especially Bertha, and could be handled without a problem! Then came my new neighbor, and when chatting with her one week, she brought up the topic of her killing a massive "cottonmouth" the other week. I realized I hadn't seen Bertha for nearly 2 weeks, and being concerned I asked what the snake looked like. She showed me picture she posted on Facebook with her phone, and sure enough, it was Bertha hacked into 7 different pieces with a shovel. I got seriously PO'd and after explaining to her that it was a harmless and beneficial snake, she insisted it had fangs and was a venomous cottonmouth. Then she went one rant on how snakes are bad and should be killed. Obviously, this wasn't the type of person you want to enjoy nature with. I left, but warned her not to touch the other snake worried that it too might cross into the wrong yard. Sure enough that one disappeared a couple week later. Then corn snakes started disappearing from my yard, and now I haven't seen a single snake in my once rodent-free yard and chicken coop for the past 3 months. Guess what? I now have a rat problem, something I haven't dealt with for the past several years.
Bah, sorry for the rant. This was recent and I guess I'm still annoyed about it, and at people who don't really have a good reason for killing things. (Not you