As others have said, evidence-based stop and search—where there is evidence and a good reason—is not in question. What is in question here is stop and search on the basis of a whim. As others have eloquently said, there is a very real danger of antagonising some groups who are already most disadvantaged, and therefore making the situation far worse.
The Government want to give the police powers to stop and search a person or a vehicle in a protest context, even when there are no grounds for suspicion. That will be permissible simply if a police officer believes that an offence—such as wilfully obstructing a highway or intentionally causing a public nuisance—might happen in the area or thinks that some people in the area might be carrying prohibited items; and there we are, back to the marker pens and knitting needles.
Protest is, by its very nature, liable to cause a public nuisance, disruption and noise, and to have specific targets, but real democratic leadership does not seek to ban opposition voices from protesting. Only a cowardly Government, who do not trust or respect their people, would take such a step.