First of all - if there really were complaints it would have to come from other whaling nations. Why would the US care about whether or not Japan wasted taxpayer money on whaling?
Secondly - did you actually have any knowledge of the topic at hand? You do know that Norway, for example, supports its whaling industry through subsidies, including to cover R&D, DNA testing, direct grants, fuel and transport costs, and general fisheries subsidies? Iceland also has direct and indirect subsidies. There is no ‘unfair advantage over all other whaling nations’.
There are various reasons for government subsidies. Some reasons are good. Some are bad. Some government subsidies are aimed at helping the development of a new technology (think solar energy, etc). Other subsidies are aimed at preserving an industry, either through short-term issues (think the government bailing out the auto industry, or the airlines after 9/11) or to prevent the industry from dying out completely (Japan has been involved in whaling for over a thousand years, with whaling mentioned as far back as the 7th century A.D.). Some subsidies are aimed at encouraging job creation. Some subsidies are pure protectionism, to be sure, and in many cases any direct benefit to that industry might be more than offset by other indirect economic costs. Which of course begs the question of how to measure the cost (if any) of potentially losing a thousand-year old tradition. For example, the US government offers subsidies aimed at native americans, including for cultural resources and national tribal organizations.
No one has yet to offer any rational reason as to why whaling is wrong. ‘Because they’re an endangered species’ is not an argument for the species being hunted, which is dominated by minke whales - essentially big cows that swim. Even the most pessimistic of estimates puts the population at around at least 650,000. Let’s suppose exactly half are female, so 325,000. Let’s further assume that just 1% of all females give birth each year. That’s 3,250 new whales a year - well below the approx. 1,700 currently killed by Iceland, Norway and Japan combined. And the birth rate is certainly higher (the average adult female minke apparently gives birth every 2-3 years).
Quite frankly, whaling in Japan specifically survives in part because of the perceived ‘racist attitudes’ on the part of predominantly Western activists - note that I haven’t seen any TV shows about Sea Shepard attacking Norweigan ships.
Imagine if China or Japan decided that they were going to protest kangaroo hunting and kangaroo meat consumption, or beef production, then turn it into a TV show. Are you sanguine as to what kind of reception that would get in the US or Australia?