As I see it there are two problems with this film. The first is the unsettling mix of humour with the holocaust. This objection is so obvious and immediate that I almost wonder if the use of humour works to some subtler end that I have not yet acknowledged. The Czech New Wave (even more than the French New Wave) often mixed humour with politics (specifically, in the case of the Czech, with the liberal politics of the Prague Spring). Here the urgency of the politics is overshadowed by intrusive physical humour and M. Hulot-esque comical desperation. An easy contrast one could make would be with the recent Romanian film 'The Death of Mr. Lazarescu,' which treats its serious topic with sensitivity and a dose of laughter to just the right measure. Just as (unconsciously?) distasteful is the moment a lingering camera turns a shocking scene of Jewish women are used as sex-slaves into something reminiscent of an exploitative brothel scene that would fit well in 'Ilsa, She-Wolf of the SS.'
The second reservation is the attempt to use fascism as a stand-in to criticize communism (a typical move to get by the censors after Prague 68). Implied in this political metaphor is the idea that the evils of fascism, by virtue of being totalitarian, are comparable in every way to the USSR. This important distinction (and the neoliberal attempt to collapse it) deserves a greater treatment than what a film rating can provide, so I turn those interested to Zizek's "The Two Totalitarianisms": http://www.lrb.co.uk/v27/n06/zize01_.html
Only slightly less a masterpiece than Hellman's other magnificent entry into the Western canon, Ride in the Whirlwind's greatest strength lies in its screenplay which supposedly is based on a collection old tales of the early West happened upon in a public library.