Here is a (maybe non-complete) list of reasons:
- As @mattiav27 mentions in the comments, the machine has moral standards, hence the machine will do not anything un-moraly to reach a greater goal. While Samaritan can stick at nothing.
- Samaritan has a lot more assets to fight with her. Clarly, Reese, Shaw and root are highly skilled, but it seems that Samaritan has hundered of assets. Also, don't forget about the challenge in S04E02 where Samaritan recruited very skilled hightly intelligent people.
- Team Machine has to hide and can only operate in the dark, while team Samaritan has assets in the government.
- The machine is a closed system, while Samaritan is open. The machine can only communite very indirectly with Finch & Co. Also, the machine deletes her memory every night (as it was mentioned in S02E21). Only root can communite directly with the machine (which is difficult in Season 4). In contrast, Greer & Co have full access to Samaritan: They can find certain people, can spy on everyone (and get every record on that -- the machine would only give a hint if there will be a murder related to that person or not), etc.