TL;DR: Yes, he was. I will focus a bit on who did not like him, why we cannot think that he was 'hated in the nation', why and for what reason it is more likely that he was loved.

When discussing Atatürk and his legacy, one always needs to remember that the man basically destroyed the Turkish version of the Treaty of Versailles without it being implemented for good. Then and now, even his opponents could not/can not deny that he led the movement that gave the country its independence. Some (some Islamists, for instance) question whether independence is worth what came after (full-scale Westernisation) or whether there could not be other ways to achieve it, but he is and was a national hero for the vast majority.

In undertaking a massive reform/revolution project like Kemalism, this helped immensely. Because, in this way, he could be seen not as a random bureaucrat imposing his vision or a lucky man who just happened to have the right father. He was the Pasha that saved the country and he was not to be opposed, though there was room for some criticism, of course, depending on the subject. It is difficult to think of what 'masses' thought around those times, devoid of devices of their own to make their voices be heard today. However, from the state archives and the press, it seems that there was never much opposition. In 1930, when a second party was launched to rival the Republican People's Party, it seemed like the people were moving in great masses towards the new opposition. However, even then, the new party could be founded only because Atatürk promised to remain disinterested and not to take a side in party politics, remaining as the supra-political President. It does seem that the economic conjuncture had more to do with the rise of the opposition than a deeper dislike of Atatürk or Kemalism.

As you note, there are exceptions. The Menemen incident is one. In December 1930, a small group of Islamists rioted in the city, killing and beheading a young officer named Kubilay, before reportedly putting his head on a lance and parading the streets. The riot was soon suppressed by force. Things were typically more complicated further East. In Dersim (modern-day Tunceli), for example, a quite large rebellion was suppressed following much bloodshed in 1937. Previous examples included the Sheikh Said Rebellion of 1925 in Diyarbakır and the Ağrı rebellion in 1930. The former probably represents the peak point of Kurdo-Islamic reaction to the new regime as it had Kurdish nationalist and Islamist motives at the same time. There were also cases of Islamists such as Atıf Hoca of İskilip being hung for treason (it is mistakenly believed that he was only hung for resisting to wear a Western-style hat following the Hat Reform of 1925). How common were these events though? It would be extremely wrong to think of Early Republican Turkey as a place of constant reaction and resistance to a new regime. More politicised Islamists and organised Kurdish resistance groups aside, it does not seem like that the majority of the people had any qualms about Kemalism besides the occasional economic troubles triggered at times by local corruption, at other times by the 1929 Crisis. When it comes to Atatürk himself, these reservations were even weaker.

Atatürk never went in public accompanied by bodyguards and that was something he was proud of, according to his own words. Part of this was, surely, the fact that by 1926 Kemalists to a great extent eliminated or pacified many of their 'dangerous' opponents such as the Unionists, Kurdish nationalists, Islamists, and communists. Yet, this surely cannot be the whole story. There are many pictures of him mingling with the public. Surely, had he been despised, there would be more assassination attempts. If the Italian secret police under Benito Mussolini's fearsome Arturo Bocchini could not prevent such attempts from taking place, surely the poorer and less equipped Turkish intelligence could not be that effective by itself. That does not by itself prove he was loved but does a pretty good job of showing that though there were discontents here and there, the myth of a large-scale discontent or even hidden rebellion in Atatürk's Turkey against Atatürk and Kemalism is more fiction than fact.

So, in short, Atatürk had many enemies. But these enemies, it seems, were never that crowded, especially in non-Kurdish parts of the populace. His reputation as the great saviour helped him a lot. As a general criticism of Kemalism, it is said that they failed to transform Turkish society to a great degree. If that is true (it is somewhat true for villages and remote towns, but those people too had to occasionally come to the cities), it is less so because these chaps had a conscious opposition to Kemalism or Atatürk (they often did not, it seems) but because the regime actually did not know how to reach those villages intensely enough with its propaganda and activities. This is not to say that Turks were enthusiastic about Kemalism as a whole. Parts of the society surely was, other parts most likely silently accepted it, with some in minority more passively-resisting than accepting. However, when it comes to Atatürk, this picture becomes even less resistance-oriented. You would not expect the abolishment of the Caliphate, the introduction of a new alphabet, the introduction of gender equality in law and much of social life, restructuring and secularisation of education to generate only a few riots here and there. I think it is pretty useless denying that part of this stems from Atatürk being actually loved. This love, in turn, seems to have stemmed in no small part from the major role of Atatürk in the Turkish War of Independence. As it was no mere fear, after his death, Turkey did not take a U-turn and to date, it is extremely easy to meet a Turk who has on his/her body a tattoo of Atatürk's iconic signature.

Sources and Recommendations on Turkey under Atatürk (that also touch upon the subject of rebellions and feelings and thoughts about him at the time):

Andrew Mango, Atatürk (İstanbul: Sabah, 2000). This book is originally published in English and I would recommend it to those who do not speak Turkish, if you can find it online though.

Erik-Jan Zürcher, Turkey: A Modern History (London: I&B Tauris, 2010).

Feroz Ahmad, The Making of Modern Turkey (London: Routledge, 1993).