I hear this a lot, particularly in arguments from the religious right. I understand that On the Jewish Question is very confusing to read because of how the word "jew" was equated with "usurer" in the 19th century leads to this conclusion - this is often used to discredit all of Marx's work.
Was he, or is this another case of misinterpretation?
To add to this, I'm going to try to explain Marx's view of religion here. Apologies if this is slightly confusing; I'm used to talking to people who have already read Marx but have some questions.
Now, "On The Jewish Question" also makes the point that one cannot abolish religion throuhg demanding atheism, without knowing the conditions from which religion springs. The text was notably written a year before Marx's "A Contribution to the Critique of Hegel’s Philosophy of Right", which starts thus:
https://www.marxists.org/archive/marx/works/1843/critique-hpr/intro.htm
Marx knew that man made religion and bows down to it, but his critique was an attempt to discover how humanity had trapped itself within inhuman forms that attempted to explain the irrational way we live, such as religion, philosophy, and political economy. Because the world of commodities & money are insane (more on that later), inverted forms of thought are needed to give them theoretical expression with 'objective' validity. (I will be speaking mostly abstractly in terms of class here, for brevity, but of course, this is why Marx called economists the theoreticians of the bourgeoisie.)
Marx in Capital does not merely attempt to say why current economic theories were wrong, but to show how they were unable to resolve apparent contradictions in themselves, because they were attempting to give a rational account of what is essentially irrational. For the shortest example, Ricardo could not resolve contradictions in the labor theory of value, because he could not see the actual contradiction (the role of labor-power and that wage-labor is inherently exploitative) within society that Marx discovered. In Capital vol III:
https://www.marxists.org/archive/marx/works/1894-c3/ch29.htm
Still, Marx had great respect for Ricardo and Adam Smith, for their work was useful in attempting to construct a consistent model of a contradictory, yet then-recently-emerging society. They were revolutionary, albeit revolutionary for the emerging bourgeoisie. As a side note, the development of criticism follows the development of society, which is why current economists (vulgar) have gone much crazier with theories like marginalism, and do not even bother to attempt a rational account, and... oh, sorry, religion. Anyway.
But political economy relates to religion and philosophy in that it attempts to show that these apparent contradictions are actually indicative of natural, human nature. Hegel, the apex of philosophy, knew that philosophy was a form of religion that attempted to give man peace with a world with which he cannot be reconciled. Philosophy does this through logic, while religion does this through faith, which makes the latter more accessible to the lower-classes: note what Marx said earlier on how religion is "logic in popular form". Both reflect the actual world in which people cannot live without illusions and must comfort themselves through the knowledge that this is natural. (Hegel's world-spirit, Adam's invisible hand.)
Like political economy, philosophy & religion cannot merely be done away with in thought (or through atheism), but through the practical reconcilation Marx spoke of through communism and the abolition of private property. This is why he called it the riddle of history solved. Now, I'm nearly finished, but religion also shares properties of capital for Marx:
https://www.marxists.org/archive/marx/works/1867-c1/ch01.htm
"Fetishism" here is not the typical way in which schoolgirl skirts arouse heterosexual men, but in an inanimate object that appears to be inhabited by a religious spirit. Man creates religion and bows down to it in thought. In reality, products are produced and appear to immediately be commodities, often owned by someone who is not the one who produced it, and whose overproduction 'causes' crisies and 'forces' people to go homeless or struggle to pay for food & the likes, despite that, obviously, it is all by our own hands.
Were the relations of humanity transparent and recognizable, we would not need special experts (like priests/economists/philosophers) to 'explain' them to us or what we are like: they would be immediately intelligible. At the end of Capital's first chapter, Marx describes communist society through the section on Robinson Crusoe's labor which is directly produced for his needs and is immediately understandable.
Now, I would always recommend people read "On The Jewish Question" themselves, but I'll end on these oft-quoted passages:
https://www.marxists.org/archive/marx/works/1844/jewish-question/
There's a line in the great Cassavetes movie "The Killing Of A Chinese Bookie" where one gangster opines that Karl Marx was wrong, and it is not religion that is the opium of the people, but money. "Money is God." A great line, but one I was always extra-amused by because Cassavettes didn't understand that Marx would have also agreed with that. One cannot simply mandate atheism without knowing where religion comes from and subsequently how to abolish it. (Which, obviously, does not mean by violence, but through it practically becoming superfluous.)
For a less abstract example of all of this, here is, lastly, Lenin explaining the attitude of the workers' party towards religion:
https://www.marxists.org/archive/lenin/works/1909/may/13.htm