What was the reason that Viceroy Gunray and the Separatist leaders were trying to kill Padmé?
It doesn't seem to make sense. She was leading an opposition to prevent the creation of an army for the Republic, which would be great to the Separatists, because they would have no one to oppose their droid army.
Instead of supporting Padmé, they are eager to kill her. Why? What's their motivation? What's their goal?
Is it just revenge for her victory in the battle for Naboo, or is it something else?
We know that Darth Sidious wanted Padme killed for her opposition to the Military Creation Act which would allow the creation of an army to fight the Separatists for the Republic. This would allow Sidious to start a war which he could use to gain even more power. Since Sidious was manipulating both the Separatists and the Republic he was in a position to put a bounty on Padme's head through the Separatists.
As you pointed out, it was not in the interests of the Separatists to assassinate Padme due to her opposition to the Military Creation Act. But Trade Federation Viceroy Nute Gunray held a strong personal grudge against Padme over the failed blockade of Naboo. Sidious no doubt inflamed this grudge and encouraged Gunray to seek revenge against Padme. Gunray's grudge was so powerful that he demanded the death of Padme as a condition for the secession of the Trade Federation from the Republic; in Attack of the Clones Obi-Wan travels to Geonosis and overhears a conversation between the Separatist leaders:
Count Dooku: We must persuade the Commerce Guild and the Corporate Alliance to sign the treaty.
Nute Gunray: What about the senator from Naboo? Is she dead yet? I am not signing your treaty until I have her head on my desk.
Count Dooku: I am a man of my word, Viceroy.
Based on this conversation, Dooku hired Jango Fett to kill Padme but Sidious had succeeded in ordering the hit through Nute Gunray (by this point, Fett and his associate Zam Wesell had twice attempted to kill Padme on Coruscant but failed).
The conversation also explains why the other Separatists supported Padme's assassination: they would benefit considerably from the addition of the droid armies of the Trade Federation. The Separatists were not aware of the clone army at the time so the addition of the Trade Federation's droid armies seemed more important than preventing the passing of the Military Creation Act -- the Separatists thought the Republic would have to raise a new army (which would take considerable time).
Later, Padme is captured along with Anakin and Obi-Wan on Geonosis and sentenced to execution. By that point, the Separatists' motivation to kill Padme was not simply due to Gunray's personal grudge against her -- by then they also wanted her dead because she knew about the droid factories on Geonosis.
We need to distinguish between 2 different occassions:
Original plot by Zam Wesell
This was ultimately orchestrated by Sidious (via Dooku via Jango Fett).
The goal was, as @Richard's comment noted, to remove a person opposing the Civil War, which was Palpatine's goal. Had Padme have her way, no G.A.R, thus no Order 66.
Sentencing Padme to death on Geonosis.
First of all, the benefit is making sure she would not tell the Republic about a hidden Separatist operation there to build droid armies.
If you recall from AotC, that place held plans to Death Star, among other things.
Second, personal grudges by Separatist leaders (Gunray over Trade Federation fiasco at Naboo)
I was rewatching it recently and while I think the answers about the viceroy holding a grudge are certainly a factor, I think Palpatine had an ulterior motive for ordering the assassination, and that he did not want her to die. It's not entirely clear when his hard-on for Anakin started, but as the Sith Lord I'm sure he had some interest in the "chosen one" and we know he has visions of the future.
I think he knew the trick to manipulating Anakin would be through his heart, and no one gets over their first crush, especially if they're brought up in a cult that doesn't allow them to fornicate. By having public attempts on Padme's life, he had an excuse to request a Jedi protector for her, and he knew she wouldn't be crazy about it, so he recommended "someone you're familiar with, an old friend perhaps, like.... Obi Wan Kenobi!" Gee, is there anyone in the galaxy who doesn't know who Kenobi's apprentice is? This way he gets Anakin close to Padme, and a little sweet talk about how she's better than sand and the rest is history (I'm justifying actions, not gonna defend this movie's dialogue)
There was also the plot to bring Anakin Skywalker to the darkside. Darth Sidious wanted to create a situation where Padme needed Anakin's protection. He knew of Anakin's one-sided love of Padme, and wanted them to spend time together, so that they would consume their forbidden love. Without this relationship, it was unlikely that Anakin would have gone over to the darkside. (The final straw was to the desire to stop Padme from dying).
