Size is not a reliable indicator of anything.
It can be.
For Military ships (ships with lots of guns) there are two fairly obvious break points.
One is at 1000 tons where you can, in theory, start mounting Bay weapons. In practical terms you probably aren't going to mount just a Bay weapon on a ship, so this moves the break point to 1500 or 2000 tons. And you can do a secondary division based upon ships of this size that do mount bay weapons from those could mount bay weapons, but don't.
The MtG2 High Guard changes this and says you can mount a 100 ton bay on a 100 ton ship, and 500 ton bay on a 500 ton ship. Other design systems (TNE, GURPS) can further break this rule.
The second is around 10,000 tons where you can start to mount spinal mount weapons. For CT-HG the absolute minimum size for Spine + power plant is around 8.5K The MtG2 HG moves this to an absolute minimum size of around 7k tons.
On the commercial side, the real world has taught us that a ship optimized for one purpose functions better than ships build to combine two. But Traveller has a long history of having ships do combined passenger/cargo traffic, at least for small ships. And given the intended ports of call for the small ships, this is entirely sensible. But at some point, as you go up the size scale, you should find the ships being optimized for either passengers or cargo/freight. Where you put this line is somewhat arbitrary, and Traveller Ship designers may not follow the lessons of the real worlds. For symmetry, I added the two military break points to the commercial side as well: 1500 tons and 10,000 tons.
At least for the commercial side the Traveller designers working within the limitations of game and economics system didn't want to have ships with a lot of crew requirements, nor too hard to pay the mortgage. The ideal Traveller game has three to six players, so a ship with that crew size is ideal. Larger crews require NPCs with requirements for care and feeding. Larger ships require more payments, which require fixed routes to travel or more assertive patrons. These interrupt the ability to have adventures. The dividing line for this seems to be around 500 tons. Smaller than this are idea for Traveller groups. Larger require more work for the Referee and players. This dividing line is entirely meta-game derived, through I could hand wave something up.
In CT-HG there is a maximum ship size based upon the TL, as set by the computer models. The MT ship system had a similar limitation, but much more obscured. Neither MtG nor T5 have a limitation on the size of the hull based on TL or other factors. (TL10 -> 10k, TL11->50k, TL12->100k, TL13->1M, TL14+ -> No limit). So when cataloging ships from earlier eras (e.g. IW, M0) or pocket empires with lower TLs, this also becomes a factor in setting classifications. Is the ship pushing the theoretical limits of the ship size based on TL?
From this I derive four size categories:
10-100 tons => Small craft
100-500 tons => Small Starships
500 - 1500 tons => Medium Starships
1500 - 10k tons => Large Starships
10K+ tons => Warships and megafreighters.
These settings in and of themselves are not the final classifiers, but serve as part of the classification system to define the groups.