The author makes the same mistake many Americans do: that the Bill of Rights was about preserving individual liberty. But the Bill of Rights was principally concerned with explicitly outlining the limits to Federal power, especially as Federal powers potentially conflicted with State powers.

That's why the First Amendment begins with "Congress shall make no law". States were of course free to makes laws respecting the establishment of religion or abridging the freedom of speech. And they did. Massachusetts, for example, made membership in a Christian church mandatory. Part of the purpose of the amendment was literally to preserve the ability for states to abridge those freedoms as they saw fit under their own law.

Similarly, this is why the Second Amendment says "being necessary to the security of a free State". "State" isn't referring to the United States or the abstract concept of a state, but literally to the various States of the new federation. The Federal constitution gave the President executive power over state militias, and Congress the power to regulate them. But what if a State wanted to use its militia to put down internal dissent (like a slave rebellion), or repel external invaders (Indians, Spanish settlers, etc) at a time when the President or Congress, for foreign policy or other national concerns, were hesitant to act? The States wanted to make sure that their militia couldn't be disarmed, or be forced to keep their arms in federally controlled depots, leaving the state entirely at the mercy of the Federal government for its self defense. Indeed, the extent to which the Federal government could control state militias was one the most contentious areas of debate surrounding ratification of the Constitution.

To be sure many State constitutions had clauses regarding freedom of speech, the right to guns, etc. But they were worded quite differently, diverse in their text and in their interpretation under State law. Importantly they were typically interpreted much less strictly--largely because it was felt that State governments were far more democratic, legitimizing any restrictions passed by legislatures. The history matters if you're going to draw grand conclusions. In as much as the Federal government today can be considered more democratic (we do elect our Senators by popular vote, now), then 18th century logic suggests we should be more tolerant of Congress directly limiting individual freedoms, at least as an abstract matter--before we get to the question of what precisely the Federal constitution permits.

It's also worth mentioning that the phrase "the people" usually referred to the people of each state as distinct bodies; and very often the people of each state as assembled and represented by their legislature. There was a strong debate about whether the United States had a singular body politic of "the people", from which it derived its legitimacy, or whether it was purely a creation of the States. At the founding the majority opinion was firmly in the latter camp. It wasn't until the Civil War that this conception had clearly shifted. Abraham Lincoln's famous line from the Gettysburg address,

that this nation, under God, shall have a new birth of
freedom--that government of the people, by the people, for
the people, shall not perish from the earth

establishes the Federal government as deriving its powers directly from, and directly owing allegiance to "the people" of the nation as a whole, without States as intermediaries. Another way to parse what Lincoln was saying was that the Federal government had a duty to protect those people--e.g. slaves--who were being oppressed by the State in which they resided. The notion that the Federal government would ever be in a position, let alone have a duty, to protect people from the laws in their own States would be, to say the least, virtually unthinkable to the Founders.