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.