All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad is His slave and Messenger.
No doubt, it is a duty for Muslims to help one another in righteousness and piety, especially concerning the matter of Da'wah (call) to Allah (The Exalted) and undertaking the public interests of Muslims and doing good to them both in religious and worldly affairs.
Here, we state that all Muslim organizations that belong to Ahlus-Sunnah Wal Jamaa'ah are in fact considered as supports for good and righteous works. All Muslim organizations take part in protecting borderline stations of Islam.
As you mentioned, no organization is free from some defect or shortcoming. This does not constitute an excuse to stop helping in righteousness and good deeds, but without any kind of bias, hate, or harboring mutual enmity.
There is no blame - Allah willing - to take part in the activities of any charitable organization that is working in the field of Da'wah and reform, righteousness and good acts, as long as such participation relates to good and pleases Allah, The Great and Almighty.
Allah knows best.