Is there any country where the founder of the nation is no longer respected?

Romulus, the legendary founder of Rome, is an example of sort. He was of course always glorified as the founder of the city, and even divinized, but at the same time he was a king, with some clear tyrannical tendencies, and during all the republic, and even at the beginning of the empire, this was enough for him to be considered as an example not to follow. It is telling that Octavian, after his victory in the civil war, refused to surname of "Romulus" that some in the senate wanted to offer him (he accepted "Augustus" instead)

Pedro I of Brazil is not venerated neither hated in Brazil.

It roots in the sui generis history of independence of Brazil, and personally of his founder and liberator.

Summarizing:

• Pedro I was born in Lisbon, Portugal, 1798.
• The Portuguese Court transferred to Rio de Janeiro in 1808, running away of Napoleon invasion of Iberian Peninsula.
• It created the sui generis situation of the capital of a Empire residing in one of its Colony, not in the Metropolis.
• His father, John VI, became King of the United Kingdom of Portugal, Brazil and the Algarves in 1816.
• In 1821, when it was safe to return, John VI went back to Lisbon.
• Pedro I declared independence in 1822.
• Portugal, ruled by his father, accepted independence in 1825. The whole process of independence was, with a few exceptions, pretty peaceful compared to the process of other countries in the continent.
• When his father died, in 1826, he also briefly reigned over Portugal, from 10 march to 2 may.
• He abdicated the Brazilian Crown in 1831 and went back to Portugal.
• He died on 1834, in Lisbon.

Therefore, despite being the de facto founder of the country, it is hard to view him as an "authentic liberator" (specially compared with the founders of the USA or Bolivar, José de San Martín, etc.), or even as an "authentic Brazilian".

In fact, despite being a national holiday, Brazilians celebrates its independence day (7 of september) way less than other countries on Americas.

Edit: it is not to say that there were not wishes of independence on Brazil. On the contrary, Brazil had separatist and republican movements since the eighteenth century. Another national holiday on April 21 celebrates Joaquim José da Silva Xavier, known as Tiradentes, executed as a leading member of the Minas Gerais Conspiracy, in 1792. Another national holiday celebrates the Proclamation of the Republic, which happened November 15 (1889). So, the ambiguous or little relevance of Dom Pedro I roots in some perception that his declaration of independence was a stratagem of the Portuguese Royal to not lose power. Usurping the authentic wishes of independence and specially of republicanism.

In Canada, Sir John A. MacDonald is today often derided as drunk and corrupt, despite his many accomplishments and notwithstanding the glowing tributes in those links. I myself am amazed that he found a compromise acceptable to the five founding provinces, and then still managed to finagle British Columbia in as well; but not all Canadians share that opinion.

Many in Quebec, and perhaps also in New Brunswick and Manitoba, still despise him for executing Louis Riel following the North-West rebellion in 1885.

Perhaps Ataturk is an example. Nowadays, his legacy is very much questioned in Turkey.

Russia's Boris Yeltsin is widely disrespected in Russia.

According to the questionnaire conducted by the request of IA Regnum in Voronezh in January 2012, 56% of the participants consider that he brought more harm than good. About 31% assessed that there was about equal amount of harm and benefit, and only 9% said that he brought more benefit than evil. Only 20% opined that he could be not that bad man in private life.

A questionnare by VTsIOM conducted by the request of state agency RIA NOVOSTI countrywide showed that only 17% of the questioned considered the deeds of Yeltsin positive, which is surpassed only by Gorbachev, whose activity is considered positive by no more than 14%.

King Clovis the I has been called "the first Frenchman", but he was more or less ignored for long periods of French history:

In April, President Chirac instructed the government to set up a national committee to mark the 1,500th anniversary of the baptism of Clovis. According to historians, the only other French celebration of the baptism of Clovis was in the 18th century, nine years before the legal separation of church and state.

However, Clovis soon became a heated partisan issue:

A lot of people even began to suspect that the Clovis debate was becoming a displaced argument about the extreme-right-wing National Front and its leader, Jean-Marie Le Pen. The Front had taken up the iconography of Clovis before anyone else, and had helped put the Clovis cult back in motion... Clovis, it turned out, had what in American politics would be called "a character problem."... Far from being a pioneering pagan-basher, was just an opportunist, who saw a way of getting papal support by triangulating himself between the heretic Arians and the pagan Alamanni.... His negatives kept going up. He was a butcher who had killed his uncles and most of his nephews... The left declared that Clovis was really more German than French... (source)

Though (or perhaps because) rightist groups have tried to generate love for Clovis, in part to celebrate monarchical over republican traditions in France, Clovis remains far from universally beloved in the almost apolitical manner that most Americans venerate George Washington.

Pedro I of Brazil declared its independence from Portugal and thus can be said to have founded the country as Brazil did not exist as an entity until its colonization by the Portuguese. He however had to abdicate his throne due to his mismanagement of the country.