After rereading a lot of the changes, something springs to mind. In order to get to my point, I have to explain a little bit about a famous and popular game.
I've played World of Warcraft for many many many years, about as long as I've played Freelancer in fact. While I consider myself fairly good at playing my class (Prot Warrior for life), there are those players out there that min/max the hell out of their stats and gear to the point where it becomes a second job for them. These players are playing at a level that the 99th percentile of players are not. However, Blizzard balances the game around the no-life players playing at the 1% which leads to a lot of fun builds being over-nerfed because they simply play them so well.
I feel like that's what is happening here with the transports. In the documentation, Haste (I'm assuming he wrote it based on the way it was written) writes that a lot of the transports can compete with ships that are built for combat. I have no doubt that Haste, or any skilled PvPer out there, in a Transport could probably whoop my ass in a VHF based on their ability alone. But your Tom, Dick, or Harry out there that sits down to simply run cargo to a destination is not. I can tell you that I am a shit PvPer and I would probably get my ass deleted by someone in a VHF on a Transport. Just the other night I nearly died to a VHF while I was flying a Gunboat. While my ineptitude flying a combat ship isn't the topic of this discussion, it does show that just because a group of people can use a ship in a combat setting does not necessarily mean that everyone can. You could say this is the case for any class of ship in the mod, but I feel like the balance with Transports vs. anything else (except the Grouse, Bulwark, and Longhorn) is an entirely different case as they are not purpose built to be able to take down a combat ship unless the player themselves are a skilled PvPer.
I don't mean to make a strawman out of the World of Warcraft example, but it does draw some parallels in my mind to this rule change. While I can see the reasons behind it in some cases (namely the thrust speed being one of them) I think it needs to be looked at closer to protect those players who simply want to do space trucking and not have to deal with being blown up by someone just looking for an easy blue.
You fear oblivion. Yet you forget. The universe remembers every atom of your being. Even dust hums your name in the dark. Roleplay is dead. Long live Powertraders and PvP I guess.