There may be a point at which any cryptocurrency (whether Bitcoin or another) is held on exchanges/wallets run by small/new companies.
How so? I mean, why do you think that such a point will occur?
If it cannot be avoided that you use an exchange, just make sure you are choosing one from among the top and most trusted. And also make sure you are not keeping your coins there. The moment you're finished with your business, pull out your coins and keep them in a storage under your sole control.
The small players have limited resources. How do they ensure they are sufficiently protected? Why don't there be hacks every other day?
Having limited resources is in fact the very reason why small players will have to protect what little they have at all cost. If it means they need to buy a hardware wallet, then they should do it. If a hardware wallet is too expensive for them, there are open-source non-custodial wallets out there that are for free. They just have to make sure they are downloading them from the official sites. They should also make sure they are keeping their seed in a very safe place outside the access of anybody else. In other words, they need to be careful in every step of the way.
Hacks do not happen everyday. A cold wallet or an open-source non-custodial wallet, careful verification in every transaction, safekeeping of password and PIN and seed, and so on will reduce the risk of getting hacked to the minimum.