It's because fees aren't calculated by the amount transacted, but by the size of the transaction. The more outputs you spend the greater the fee will be. Remember, the miner just includes data in a block and is incentivized to mine what pays more, regardless of the amount the people transact.
to clarify and correct.
1. fee's are not fixed to transaction data size. you can actually choose any value you want as a fee. the amount you pay is a calculation of how much you think is fair to put to get your transaction seen and included into a block, the less you pay the longer you wait.
2. miners do not include data into blocks. we are not in solo-mining era of 2009-2011. miners in the current era are ASICS that just compute the blockheader(non transaction data) into a complex hash by a degree of difficulty.
ASICS run 24/7 whether there are 0 transactions or thousands. whether there are fee's or not.
3. POOLS (a separate entity to miners) manage the block content cumulation. and its the pools which decide what transactions they feel worthy of including. there is no hard rule that says they have to accept highest fee first. thats just pure economic human choice of greed decision.
4. yes a laymans suggestion is that you should pay more if your data is bloaty with many inputs and outputs, and pay more if you want to persuade a pool to include your transaction sooner. but this is not a guarantee.
some people only put in small fees because they are not too bothered about when their transaction will confirm.
some people put small fees when handling large value to purposefully give themselves more time and opportunity to RBF if they made a mistake when broadcasting a transaction