Why did the Pharisees' religious activity not count with God?

Their religious activity did not count because they were ignorant of the things of God, having zeal but no true knowledge. Their self-righteous robes, public praying, and belief they served God were rooted in ignorance, not lack of intelligence, but simply never having been taught God's truth.

Les explains that these Jews had a zealousness for God and were religious—the Pharisees with their self-righteous robes and public praying thought they were doing God a service, but they had no knowledge and were totally ignorant of the things of God. In verse 3, Paul uses the word 'ignorant.' Les qualifies that ignorance does not mean a lack of brain power; a brilliant person can still be ignorant of a subject never taught, like electricity. These Jews had simply never been taught God's truth, so their religious activity lacked the knowledge that counts with God.

Romans 10:3

For they being ignorant of God’s righteousness, and going about to establish their own righteousness, have not submitted themselves unto the righteousness of God.

What did the Pharisees think they were doing for God, and what was their problem?

The Pharisees thought they were doing God a service through self-righteousness, religious robes, and public praying. Their problem was not a lack of brain power but a lack of knowledge: they were totally ignorant of the things of God because they had never been taught, as Paul says, “being ignorant.”