Yes, there were concerns over, what appeared to the colonials as the arbitrary establishment of the Catholic faith as a state religion in the Quebec Act, and it was included by many of the founding fathers as an argument (or a scare tactic) when discussing the intolerable acts. Some of the founders had expressed anti-catholic sentiment even before the Quebec act, but you have to look for the relevant term from their time: Popery.
Both Samuel and John Adams spoke out, even before the Quebec Act against popery:
From The American Historical Review:
Samuel Adams in 1768 "verily believed" that "much more is to be dreaded
from the growth of Popery in America than from Stamp Acts or any other
Acts "destructive of mens civil rights" He thought one should be very
cautious in talking about popery before youth lest unwittingly one
should speak "the language of the Beast" John Adams too was alarmed (1771) that "the barriers against popery erected by our ancestors are
suffered to be destroyed to the hazard even of the Protestant religion."
This concern among the Protestant faithful, and its use to stir up the populace, was also noted in the Historical review article:
It was worthy of St Ignatius as Brooks Adams says the way Samuel Adams
used the toleration granted the Canadian Catholics by the Quebec Bill
as a goad wherewith to inflame the dying Puritan fanaticism Holy water
and papal bulls were special objects of Puritan hatred and Adams made
his fellow citizens fear that they were in danger of both.
More discussion of the anti-popery sentiment among patriots can be found in a more recent publication, Papist Patriots: The Making of an American Catholic Identity By Maura Jane Farrelly
In the able hands of the Patriot leadership, the Quebec Act became the
proverbial straw that broke the camel's back, the final sign that the
king had become irredeemably corrupt.
Another recent publication Anti-Catholicism in America, 1620–1860
also by Maura Jane Farrelly, has an excellent discussion of what the term 'popery' meant to the colonists:
When he used the word, Adams meant both a cause and an effect of
tyranny. Popery was the result of injustices like the Stamp Act, but
it was also the fertile soil in which such injustices could be
planted.
Alexander Hamilton also expressed his concern over this aspect of the Quebec Act. The Works of Alexander Hamilton, pg 39:
Does not your blood run cold to think that an English Parliament
should pass an act for the establishment of arbitrary power and Popery
in such an extensive country. If they had any regard to the freedom and
happiness of mankind they would never have done it. If they had been
friends to the Protestant cause they would never have provided such a
nursery for its great enemy they would not have given such
encouragement to Popery. The thought of their conduct in this
particular shocks me. It must shock you too my friends. Beware of
trusting yourselves to men who are capable of such an action. They may
as well establish Popery in New York and the other colonies as they
did in Canada. They had no more right to do it there than here.
The concern was not just that of some of the leadership at the times, but was also expressed or felt by many of the common individuals as well. (From The American Historical Again):
When we find bigotry like this in the minds of American leaders we are
not surprised that a favorite device on the banners carried by Puritan
mobs after the Quebec Act was the demand "no Popery" and that one of
the motives animating the captors of Ticonderoga was to secure the
colonies from the incursions of the Roman Catholics "those children of
darkness".
Even in areas which were strongly Loyalist, the popery clause became an issue. For example, in New York in 1775 there was a flag created in protest and raised on a Liberty pole in the center of New York. This flag, known as the George Rex Flag, contained the words:"GEORGE III REX AND THE LIBERTIES OF AMERICA. NO POPERY".
So, no matter what the intent of the act was, the Protestant majority definitely expressed concern over what was perceived as the King establishing an official state religion in Canada, and as Hamilton put it:
Beware of
trusting yourselves to men who are capable of such an action. They may
as well establish Popery in New York and the other colonies as they
did in Canada.