TL;DR: Because Palpatine/Sidious told him to take care of the Jedi first.
From the script.
Prior to the flight to Tatooine, Amidala has suspicions about an invasion, but still believes that negotiations are still possible with the Trade Federation.
CAPT. PANAKA : Check the transmission generators...
BIBBLE : A malfunction?
CAPT. PANAKA : It could be the Federation jamming us. Your Highness.
BIBBLE : A communications disruption can only mean one thing. Invasion.
AMIDALA : Don't jump to conclusions, Governor. The Federation would not dare go that far.
CAPT. PANAKA : The Senate would revoke their trade franchise, and they'd be finished.
AMIDALA : We must continue to rely on negotiation.
Captain Panaka explains why they're only trying to capture Amidala.
CAPT. PANAKA : They need her to sign a treaty to make this invasion of
theirs legal. They can't afford to kill her.
Palpatine/Sidious knows that the Republic won't do anything about the invasion.
PALPATINE : ...the Republic is not what it once was. The Senate is full of
greedy, squabbling delegates who are only looking out for themselves and
their home sytems. There is no interest in the common good...no civility,
only politics...its disgusting. I must be frank, Your Majesty, there is
little chance the Senate will act on the invasion.
NUTE : The invasion is on schedule, My Lord.
DARTH SIDIOUS : Good. I have the Senate bogged down in procedures. By the
time this incident comes up for a vote, they will have no choice but to
accept your control of the system.
From the very beginning of the movie, the Trade Federation has attempted to kill the Jedi (seemingly on their own, as no orders from Palpatine/Sidious are mentioned) and failed.
Obi-Wan and Qui-Gon have discovered the invasion fleet.
QUI-GON : Battle droids.
OBI-WAN : It's an invisible army.
QUI-GON : It's an odd play for the Trade Federation. We've got to warn the
Naboo and contact Chancellor Valorum. Let's split up. Stow aboard separate
ships and meet down on the planet.
Sidious explains to the Trade Federation that Maul is to kill everyone except Amidala (again, because he needs her to sign the treaty)
DARTH SIDIOUS : Destroy all high-ranking officials, Viceroy ...slowly...quietly. And Queen Amidala, has she signed the treaty?
NUTE : She has disappeared, My Lord. One Naboo cruiser got pat the blockade.
DARTH SIDIOUS : Viceroy, find her! I want that treaty signed.
NUTE : My Lord, it's impossible to locate the ship. It's out of our range.
DARTH SIDIOUS : ...not for a Sith...
A second SITH LORD appears behind DARTH SIDIOUS.
DARTH SIDIOUS : (Cont'd) ...Viceroy, this is my apprentice. Lord Maul. He will find your lost ship.
Finally, Palpatine/Sidious tells Maul to kill the Jedi first, so that he may kidnap Amidala.
DARTH SIDIOUS : Move against the Jedi first...you will then have no
difficulty taking the Queen back to Naboo, where she will sign the treaty.
So, Maul is not sent specifically to kill two Jedi; he is sent to kidnap Amidala and kill everyone in the way.