Excellent point. Let's say you have a kid like Homer Bailey who got a generous bonus and is probably making way better money than the average minor leaguer is making. Does his salary count too?
Take Matusaka's situation too. None of the money that BOS paid the Japanese league to get his rights and sign him was salary. He's making around $10M a year, IIRC. That's expensive but it's only $1M more than what Milton makes. You make a $100M cap, the rich teams are going to be all over this Japanese and Cuban thing. They rake in so much revenue yet only have to spend $100M on salaries. What are they going to do with the rest? If you are in favor of a salary cap, do you like a hard cap where it counts against the cap to re-sign your own free agent like the NFL or a soft cap like the NBA where it doesn't?
A salary cap isn't going to make players like A-Rod come to Cincinnati or Pittsburgh or KC. If he were a free agent and there was a cap problem, the Yankees could sign him for as much as they could and then they could defer salary or YES could hire him as a mulit-million dollar "consultant." Yankees pay A-Rod $15M and YES pays him $10M.
Let's say the Reds are at or near the salary cap ceiling but they need another pitcher down the stretch. The guy is going to cost the Reds big bucks but if the Reds trade for him, they are going to be over the cap. You can't blame ownership again for not wanting to bring an expensive player in. The cap is the culprit in this case.