Absolutely! They had to. But keep in mind that the anti-Masonic party came about early in the 19th century. Men who were in their teens during the Revolutionary War were now statesmen, so there was still a tremendous amount of awareness of the individuals who founded the nation as individuals. They hadn't yet melted into that general mass of "founding fathers."

However, what they generally sought to do was:

1. Cast doubt on the extent of the involvement of the supposedly few good men in the Fraternity.
2. Focus on the politicians who were not protected by the shield of popular acclaim.
3. Seem to come to the aid of the reputation of the most acclaimed members of the Fraternity in order to salvage their reputations which had been "tarnished" by the association.

You can see all of this at work in the political screed, Vindication of General Washington from the stigma of adherence to secret societies by Joseph Ritner and which was delivered to the US House of Representatives in 1837.

Here's a small taste:

That Washington was an initiate we do not doubt, as many other respectable individuals have been ... for it has been the policy of the detestable, murderous society to seduce into their ranks the most respectable members of society and then to bind them to the most shocking, anti-Christian oaths [and] to keep the secrets of the institution, which chiefly consists, like a band of pirates and robbers, of the signs by which they may be known to each other! It is hardly necessary to add that of 100 initiates 99 though bound by their oaths to silence, have little more to do with the institution, although claimed as a member and "brother." Such were "brother Washington," "brother Judge Marshall" and a great number of others, who have been hypocritically brought within the pale of Freemasonry."

Outside of the hyperbolic language, you can see here the desperate attempt to cast the heroes of the Revolutionary War as "not really Freemasons". But, of course, nothing could be further from the truth. Washington founded his own military Lodge, after all!

It goes on to talk about Lafayette, a French Freemason who was one of Washington's most trusted generals:

It is one of the Masonic deceptions in permitting the public to believe that the corner stone [of the Bunker Hill monument] was laid by La Fayette, whereas he was only a spectator. It is engraven on the plate thus "On the 17th day of June, 1825), at the request of the Bunker Hill Monument Association the Most Worshipful John Abbott, Grand Master of Masons in Massachusetts, did in presence of General La Fayette lay this corner stone of a monument," &c.

And that's just the forward to the actual speech!