The way the human brain works, its easy to perceive things that aren't there.
Can I recommend that you download equilab (free) and play around with hands and you will see that "crazy" situations really aren't quite as crazy as we perceive them to be.
In the example you have given,
Preflop you had a 12% chance of winning (assuming you are only playing against 1 opponent - if you add in other opponents, your equity falls) and your opponent has 88% equity.
You have a great flop which boosts your equity to something like 75%. That sounds a lot, but if you break it down, it means that if you play the hand 4 times, you will expect to win 3 and expect your opponent to win 1. AT this stage it is not "crazy" if your opponent wins that 1 in 4.
By the turn you are in a really strong position and have about 95% equity. However that still means that your opponent can expect to win 1 time in 20, still not "crazy" if he does go on to win, as he in fact did.
1 time in 20 means that if you play 20 situations such as that, you should expect to lose 1. If you play 200 situations like that, you should expect to lose 10. By the time you play 2,000 situations like that, you should expect to lose 100!! It keeps happening, as it should.
I know it can seem tough when you're starting out, but you need to embrace it, understand it and ultimately you can beat it. The "variance" is irrelevant if you are playing within your bankroll - sometimes it will go in your favour, sometimes it will go against you, but if you play enough hands, then there will be no luck/variance, it will all balance out.
Think of the hands you lost when you were ahead, and compare the odds to the number of hands you played it probably doesn't seem quite as crazy if you analyse it properly.