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An Act of Worship
Having good thoughts of Allah is an enormous act of worship and has a high position for those seeking to get close to Him. It is one of the obligations of Tawheed. In fact, the Tawheed of the slave will not be correct except by having good assumptions of Allah. 
 

Allah SWT says, “I am as my servant thinks of Me.” [Sahih Muslim]

 

Al-Qadi reports that it has been said to mean the servant will be forgiven when he seeks forgiveness, his repentance will be accepted when he repents, he will be answered when he supplicates, and he will be sufficed when he asks for what he has to be sufficient for him. It has also been explained as hope and expecting to have one’s sins pardoned, and this is more correct.

The following explanation is from ʻAbd al-Raʼuf al-Manawi’s book, Fayd al-Qadir: Allah SWT says, “I am as my servant thinks of Me.” Meaning, if he thinks good of Me, I will treat him well, and if he thinks bad of Me, I will treat him badly. 

Ibn al-Qayyim said: One of the greatest sins in the sight of Allah is to assume the worst and have bad thoughts about Him. Were someone to think badly about Allah, they would have assumed things about Him that contradicts His holy perfection and that contradicts the reality of His names and characteristics. Having good thoughts about Allah will produce good actions; and this comes from having knowledge of Allah – one is the result of the other.

If you know the Name of Allah, Al-Ghaffaar, then you have to perfect your thoughts about Him when you make istighfar. If you deeply ponder upon His Beautiful Name, At-Tawwaab and that Allah will accept the repentance of His servants and pardon them for their offences, then it is upon you to perfect your assumptions of Him, that He will accept your repentance regardless of what your offence is.

It has also been said that there is no sin so great before The Judge that it should cause you to despair of thinking good about Allah SWT. Whoever truly knows his Lord, he would know his sin is insignificant when compared with Allah’s generosity.

A Warning Against Losing Hope
Jaabir (RA) said, “Three days before the Messenger (PBUH) passed away, he said, "None of you should die except while he is having good thoughts about Allah." [Sahih Muslim]

Scholars have said that this is a warning against losing hope and despairing of Allah’s mercy, and an encouragement to have hope especially at the time of death. An individual should expect Allah to have mercy on him and pardon him. Some scholars have also said that during times of wellbeing and health, an individual should have both hope and fear in Allah and these two feelings should be equally balanced.

Others say that one’s fear should be more, but when the signs of death approach, a person’s hope in Allah’s mercy should become stronger. This is because the very purpose of having fear of Allah is to prevent oneself from committing sins and ugly deeds, and to increase in obedience and good deeds. And those things are most often not possible during the last moments of one’s death.

Instead, in that situation, assuming good thoughts about Allah is preferable. It would cause one to have feelings of destitution and submission and to feel oneself in total need of Allah SWT.

When Allah allows calamities to take place in the world, one should have good thoughts about Allah, that He, The Majestic and Most High, only lets these calamities occur for a great and huge wisdom. One should have good thoughts about Allah with regards to whatever Allah SWT decrees in this world and with regards to everything that He has legislated upon the tongue of His Messenger (PBUH); that it is something good and a benefit for all of the creation, even if some people are unable to comprehend this benefit and the wisdom behind what He has decreed.

It is upon all of us to submit to the decree of Allah, Exalted is He; the legislative and the universal, and that we have good thoughts about Him because He, Glorified and Exalted is He, is the One deserving of all praise and glorification.
 

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Sources: Authentic Translations