Because transporters don't help you keep the balance or fight off the Klingons, Romulans or whoever else, when they come for you with their fleet.
And because you need starships and their facilities to explore unknown regions of space. You can't keep beaming people blindly hoping to hit a planet.
Then why didn't Admiral Robocop just beam a bunch of nukes to all the Klingon planets? How could they prove who did it?
He wanted to cause a war. Why do you think he had the Enterprise sabotaged?
Hiding who attacked Kronos was never part of his plans.
He wanted to win the war. Harrison beamed 72 missiles with a single transport on a starship. 72 missiles over Qo'nos would devastate the planet - or better yet, just blow up Praxis - that's just a small moon. A Taste of Armageddon featured tech to beam missiles within the same system from one planet to another. We can assume that this WAS S31's plan and this was why they were targeted.
It is a crazy can of worms to open.
I'm way more in favour of having clearer defined limits to the tech on all sides, with some having a minor advantage in some respects like Klingons having more manoeuvrable ships with more powerful weaponry but weaker shields and less powerful warp drives etc.