If miners are not having profit, they would have shot down operation and never mine but the hashrate rate continue to increase which means either more miners are joining and old miners are buying more mining equipments.
About the issue of if the transaction fee is never enough, this can happen if the mempool is congested, that is why it is good to use RBF in case of such time so that you can be able to increase the fee if such situation happen.
Aye, but currently we are operating on block rewards, eventually (a long bloody time) block rewards won't be around, and therefore they will be operating on the fees that the users include. Unfortunately the only answer that seems plausible is that fees either increase so much that it justifies mining or the amount of miners drops massively, and therefore the difficulty. So, only a few miners would be needed to process the transactions. Obviously, this is all so hard to predict, because by the time this becomes a reality, we don't know how popular Bitcoin is going to become. If Bitcoin becomes one of the mainstream currencies, being used every day by millions or dare I say it; billions of people then I don't think miner incentive is going to be a problem, we'll likely have far more greater problems though.