Motorcyclists at the rally said the majority were responsible
North Wales Police has defended its policy of stopping motorcyclists - saying it has helped save lives.
It comes as hundreds of motorcycle campaigners protested, claiming the sheer numbers of riders being stopped put off bikers visiting the area.
The British Motorcyclists' Federation (BMF) said police were "using a sledgehammer to crack a peanut".
But the force said the Operation Focus checks had "undoubtedly" brought the number of road deaths down since 2008.
Motorcyclists were riding in north east and north west Wales on Sunday in a Reclaim North Wales protest, organised by the magazine Motorcycle News, to highlight the issue.
They estimated 3,000 bikers took part, although police could not confirm numbers.
The BMF have called the stop check policy "clumsy" and likened it to stopping football fans just because they like football.
Jeff Stone, from the BMF, said: "Ordinary, everyday motorcyclists just going for rides on the beautiful roads of north Wales find themselves harassed by police.
"We fully accept there are problems, like in any sector of society, of some people - the nuttier end if you like - who are going too fast, in the wrong places and causing accidents. But that's not the majority.
"It's using a sledgehammer to crack a peanut. They wouldn't dare do it if they said they would be stopping every blue Mondeo on the road."
Mr Stone said he wanted more policing but for it to be targeted on those breaking the law on the roads.
Chief Inspector Gary Ashton from North Wales Police, who is responsible for road policing, said the "peanut" being talked about was road deaths.
"People are losing their lives," he told BBC Radio Wales.
"In 2007, 12 motorcyclists died on the roads of north Wales, in 2008 eight more than that died, so that's 20 in two years.
"But this year we've seen a reduction and while it's unfortunate for any loss of life it's only two compared to the large figures we've seen before."
He said there were some intent on coming to use the roads as a racetrack and the policy was aimed at offering advice on risks and information.
In 2006, North Wales' then chief constable Richard Brunstrom compared two motorcyclists filmed from a helicopter riding at nearly 100mph to an "episode of the Wacky Races cartoon".
Last year, all four Welsh police forces pledged to use helicopters, unmarked cars and camera bikes to cut motorcycle-related deaths.
A total of 43 bikers or their pillion passengers were killed in Wales during 2007, the highest total since 1984.
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