I’m scared to value bet 2 pair on the flop a lot of times heads up because so many players are folding to c bets , should I bet anyway?
There's nothing wrong with betting a strong hand and getting folds. When we 3bet pre flop and it comes Kxx or Axx, we should just bet, even if we flopped the nuts. It's painful when we get folds, but we don't just have monster hands here. We have AA AK AQ AJs TT-QQ maybe some other Axs, we can get value from A7 78s 99 etc, and we get folds sometimes when we're behind to 66. Checking in this spot is actually a strong line to take. If I were villain, I'd proceed with extreme caution when hero checks Kxx in a 3bet pot. I'd be worried about KK.

When a player utg or early position min raises to 0.04 how should I read that as weak play or trying to rig the pot?
It depends on the villain. Generally, early position raises are stronger than late position raises, even when it's a minraise. Adjust your range accordingly, play with caution. Some villains are playing too loose in early position, make a note if someone shows up with 56s or something like that after minraising early position so you know not to give the guy too much respect. Without knowing they are positionally bad, assume it's a decent hand.

Also if I had a very strong hand in position do I maybe want to make it less than 3x
Don't get into the habit of raising strong hands less than weak hands, this is an excellent way to turn your cards face up. If you're reraising x3 with K7s but x2 with AA, someone is going to notice. Just keep it standard, make it the same regardless of your hand. This is balance, you want villains to have as much difficulty as possible putting you on a range.

When 3betting pre flop, just make it x3. If you're 4betting, you can make it a little less, maybe x2.5, but minraises should generally be avoided because we won't get folds, which makes it difficult to reraise as a bluff.