John, Martha and Rebecca were leaders in the community. They were respected and even feared for their outspoken and direct criticism of other leading members of Salem society. As such, they had many enemies and it can thus be expected that when the accusations of witchcraft were lodged, they would be targeted. It was a method by which their enemies could take revenge.
To clarify why they were specifically targeted as the main suspects, one needs to scrutinise each of the three individually and look at their positions, relationships and influences within the broader Salem community.
In his notes, Arthur Miller provides the following description of John:
Proctor was a farmer in his middle thirties. He need not have been a partisan of any faction in the town, but there is evidence to suggest that he had a sharp and biting way with hypocrites. He was the kind of man - powerful of body, even-tempered, and not easily led - who cannot refuse support to partisans with-out drawing their deepest resentment. In Proctor’s presence a fool felt his foolishness instantly - and a Proctor is always marked for calumny therefore.
Proctor was particularly bitingly critical of two leading members of Salem society: the parish priest, Reverend Samuel Parris, and the son of the richest man in the county, Thomas Putnam, who was a wealthy landowner. Proctor had been particularly critical of the Reverend's repeated attempts to enrich himself at the cost of his parishioners. One such example was the Reverend's insistent request for gold candlesticks on the pulpit, which the parishioners obviously had to pay for. The other was the good Reverend's unrelenting request for the title deeds to the rectory.
These actions by Reverend Parris disturbed John so much that he turned from the church and attended services irregularly. His continuous critical commentary about the Reverend's materialism made the paranoid Parris believe that he was part of a faction which wanted to oust him. Therefore, when the witch trials commenced and John was arrested, the Reverend consistently meddled in the court's affairs trying to further implicate him. It is for this reason that he was deemed a leading suspect.
John had also severely criticised Thomas Putnam for his claims to land that John believed did not belong to him. Early in the play, there is an altercation between the two men in which Putnam lays claim to timber that John had removed from property which he said was his, willed to him by his grandfather. John rejected his claim and Putnam threatened either violence or legal action. Thomas Putnam used the trials to get rid of those who he felt had denied him right to his property. Since John Proctor was one such, he gleefully supported his arrest, since an enemy would be removed.
Martha was the wife of Giles Corey, a man who had been blamed for practically everything that went wrong in Salem. He was a brave man, truculent and stubborn, who would take to court anyone at the slightest provocation. As such Giles was seen as a threat and a nuisance. To get back at him, his enemies implicated his wife. Furthermore, because he was naive, Giles at times said the wrong things at the wrong time. He unwittingly implicated Martha, for example, when he mentioned that whenever she read from her books, he could not say his prayers. Although he tried to withdraw what he said later, the damage had already been done. Martha was seen as a main suspect mostly because of her husband and his influence.
In his notes, Arthur Miller has much to say about the Nurses and their ongoing battle over land, with especially the Putnams.
Rebecca was the wife of Francis Nurse, ... and Rebecca also enjoyed the high opinion most people had for him. By the time of the delusion, they had three hundred acres, ...
... to explain the systematic campaign against Rebecca, and inferentially against Francis, is the land war he fought with his neighbors, one of whom was a Putnam. This squabble grew to the proportions of a battle in the woods be-tween partisans of both sides, and it is said to have lasted for two days ...
Ruth Putnam hated Rebecca and resented the fact that Rebecca was so respected in the village, and that she had given birth to so many healthy children while she, Ruth, had so many die in childbirth or soon after. The witch-trials were an ideal opportunity for her to get back at Rebecca. Her husband, Thomas, could also have his vengeance and profit from Rebecca's arrest and eventual execution.
The three were placed high on the list of suspects mostly because they stood in the way of whatever their enemies wanted to achieve. They were a risk, and with them out of the way, their opposition could do whatever they wanted, with no or very little resistance.