Obviously, a tax has the significant advantage of providing money to the government, something that a ceiling simply does not do. Unsuprisingly, many presidents would prefer to have more money to allocate to their preferred budgetary purposes. In Roosevelt's case, this was World War II. Roosevelt all but said this explicitly in his April 27, 1942 fireside chat:
Are you a business man, or do you own stock in a business corporation?
Well, your profits are going to be cut down to a reasonably low level
by taxation. Your income will be subject to higher taxes. Indeed in
these days, when every available dollar should go to the war effort, I
do not think that any American citizen should have a net income in
excess of $25,000 per year after payment of taxes.
As always with politicians, it's difficult to say what his true motivations were. However, though Roosevelt is largely remembered for his social programs, he also was very dedicated to the American war effort, so this wouldn't have been out of character for him.
Inflation was also a concern. Roosevelt's treasury used this as an argument for the tax:
In late 1943, Treasury Secretary Henry Morgenthau asked Congress for
another tax increase. He framed his appeal, in large part, as an
anti-inflation effort. The new act, he argued must help stop
inflation. "[N]othing in the economic field can interfere with the war
effort as much as an uncontrolled rise in prices," he told the House
Ways and Means Committee. "An inflationary price rise is a source of
grave social injustice. It undermines morale and impedes war
production. It strikes at random without consideration of equity or
ability to bear the hardships which it imposes. Once it has acquired
momentum, inflation is extremely difficult to control, and leaves a
heritage of post-war stresses and strains that will haunt us for
Now, if a direct wage ceiling were imposed, companies, unable to spend that money on attracting more highly-paid CEOs, might spend it on competing for labor lower on the company totem pole. This would lead to more money in the pockets of somewhat lower-paid workers, which might be a nice thing for income inequality, but could lead to excessive spending and spur on inflation. I'm not sure how plausible this justification is, though: since the taxes were intended to be put back into the economy through military spending, it's possible they could have had the same effect.