I'll try to present my case by comparing the bonjwas/high end players for each race (by posting my race rankings and my top 10 all time ranking). My rankings are obviously subjective, that said i think my list is fairly accurate (i factored in player accomplishments and peak skill level as a secondary parameter). My main goal is not to discuss whether or not X player should be ranked 4th instead of 5th, it's to show the amount of dominant players/bonjwas that each race has had throughout the history of the game.
Even tho players like BeSt and Soulkey were very high level players at their peak i decided to leave them off my list. The impact they left on the game (in terms of individual accomplishments) is negligible but they were both very good players nonetheless. ChoJJa also deserves a shoutout, some people might have him #6 instead of GoRush but again that's pretty irrelevant to my main argument. The lower end people on my list are more of an honorable mention more than anything, a lot of those players are interchangeable.
I based my rankings on player accomplishments but i also factored in individual skill levels. For example Bisu isn't your typical tier 1 bonjwa but i consider him one due to his skill level and overall body of work (3 MSL titles, overall winrate, performance in non premier/major tournaments such as IEF etc.).
Another detailed list with player accomplishments: http://www.teamliquid.net/forum/brood-war/526706-all-time-bw-player-rankings-a-balance-discussion#9
Personal race rankings:
Terran = 1) Flash 2) NaDa 3) iloveoov 4) BoxeR 5) FantaSy 6) XellOs
Zerg = 1) Jaedong 2) sAviOr 3) Julyzerg 4) YellOw 5) EffOrt 6) GoRush
Toss = 1) Bisu 2) Stork 3/4) Nal_rA/Jangbi 5/6) Reach/Garimto
I'm sure everyone can agree that the best player of each race is Flash, JD and Bisu. That said, if you look at their individual accomplishments it's clear that Bisu is way behind JD and Flash.
Now look at the 2nd best players for each race. You can argue that Stork and FantaSy (easy comparison to make because they were rivals) are pretty much in the same tier in terms of accomplishments/overall level of play (i'll give the edge to Stork but the gap isn't huge tho, FantaSy was peaking towards the end of the KeSPA era).. but FantaSy is ~the 5th best Terran player whereas Stork is easily the 2nd best Protoss. Of course Stork isn't comparable to players such as NaDa/iloveoov or sAviOr (and possibly July), all those guys left a huge mark on the game.
Now let's look at the 3rd best players for each race. We have iloveoov for Terran, sAviOr for Zerg (some might argue that July deserves to be #3 due to what happened with sAviOr) and Jangbi or Nal_rA for Protoss (again, debatable #3/#4 ranking for Toss). Jangbi and Nal_rA have had great careers but can anyone honestly say that they're comparable to July/sAviOr, iloveoov or BoxeR (in terms of the impact they've had on the game)? Nope.. and it really isn't close imo.
Now let's look at the top 10 greatest players of all time. This list is subjective (for example you can have Bisu at #3 and NaDa at #4, some people might even have iloveoov at #4 and Bisu at #5) but the point i want to get across is how little impact Protoss has made compared to the other races throughout the years.
Statistically Zerg hasn't fared too well either but their top 3 players were extremely dominant. sAviOr and July left their mark on the game, they were both bonjwas during their peak.
Top 10 all time rankings:
1) Flash 2) JD 3) NaDa 4) Bisu 5) iloveoov 6) sAviOr 7) BoxeR 8) July 9) Stork 10) FantaSy
So we have 5 Terrans, 3 Zergs and 2 Protoss'. Personally I consider the top 8 players to be bonjwas (which makes for 4 Terran bonjwas, 3 Zerg bonjwas and 1 Protoss bonjwa) because they each have 3 major titles and they were all extremely dominant players during their peak.
We can expand the discussion and talk about current gameplay balance (related to game mechanics) as well.