If I sent 0.002 or 0.005 from wallet to binance for exchange, I only pay a transaction fees from my wallet while the exchange platform (binance)didn't charge me anything.
That's because you are depositing to Binance, and there are no deposit fees on that exchange. If you make a trade with those coins, Binance will charge you trading fees. If you withdraw them, they will charge you withdrawal fees.
Binance get money from many means like trading fee, withdrawal fee (which is far more than the actually transaction fee), ads display for p2p, IEO and few other ways.
You are forgetting one very important way to make money for exchanges: listing fees for altcoins and shitcoins. Those aren't cheap. It's the dream of every altcoin developer to get listed on Binance because they know the amount of traffic and trading activity that takes place on that exchange. Unless the coin has strong fundamentals (many don't), where Binance sees it as an advantage to add support for it on their platform, they will negotiate with the devs and charge them a hefty listing fee.