Choosing the biggest flop as your benchmark is a very poor argument. If you lose half as much money as Marathon, you're technically twice as good, but it's still a flop and investors and publishers want successes, not half flops.

Marathon existing does not justify the investments into new RTS games. Quite the contrary. Marathon got hundreds of millions in cash because the shooter genre was making billions (at the time) so for them it was worth the gamble even if they lost. But the RTS genre is not making nearly enough money to justify Marathon levels of gambling on new IPs.