Firstly: 

To begin with, we would like to congratulate you for these good intentions and keenness to offer the obligatory prayers in congregation. We ask Allaah to make you steadfast in adhering to Islam and righteousness, and we pray that your father’s actions will not put you off from doing what is right and following true guidance. Before answering your question, we should mention a very important matter, which is:  

Honouring and obeying one's parents has been enjoined by Allaah in many places in His holy Book, such as the verses in which He says (interpretation of the meaning): 

“Worship Allaah and join none with Him (in worship); and do good to parents …”

[al-Nisa’ 4:36] 

“And your Lord has decreed that you worship none but Him. And that you be dutiful to your parents. If one of them or both of them attain old age in your life, say not to them a word of disrespect, nor shout at them but address them in terms of honour.

24. And lower unto them the wing of submission and humility through mercy, and say: ‘My Lord! Bestow on them Your Mercy as they did bring me up when I was young’”

[al-Isra’ 17:23, 24]

Obedience to parents is obligatory, unless they tell you to disobey Allaah, in which case you are not obliged to obey them, because the Prophet (peace and blessings of Allaah be upon him) said: “There is no obedience if it involves disobedience towards Allaah, rather obedience is only in matters that are right and proper.” Narrated by al-Bukhaari, 6830; Muslim, 1840. 

With regard to prayer in congregation, this is obligatory, and it is not permissible for a father to forbid his son who has reached the age of maturity to do it. Rather parents should enjoin their sons to pray in congregation and encourage and urge them to do so. If the father notices that his son is falling short in that regard, then he must make him aware of his responsibilities and remind him that he will be questioned about it before Allaah on the Day of Reckoning. So he should enjoin what is right and forbid what is wrong, and remind those who are under his care of their duties towards their Lord and the seriousness of neglecting those duties.  

If the father falls short in his duties towards his children by not enjoining what is good and forbidding what is evil, or encouraging them to do good and warning them against evil, this does not absolve them (the sons) of sin if they fall short in their duties or commit haraam actions. 

If the father forbids his sons to perform a duty that has been enjoined upon them by Allaah, in that case they do not have to obey him by disobeying Allaah or by forsaking that which Allaah has commanded. If the father tells his son not to offer all or some of the prayers in congregation, then he has told him to commit a sin, and this case he is not to be obeyed, but at the same time he should be treated with kindness and respect. 

With regard to your question about going secretly to pray Fajr, this is good on your part, but it is treating your father badly without realizing it. You father is committing a sin so long as he forbids you to pray in congregation, and even if you go out secretly, the burden of sin is not lifted from him, because he is still telling you to do something wrong and forbidding you to do something good, even if you go out to pray without his knowledge. So you have to try to convince him of the Islamic ruling, even if you get someone else to do it, if he will not listen to you or he thinks you are too young. If he does not respond, then there is no sin on you if you go out without his permission or knowledge, but you have to be very careful when going to the mosque.

Secondly: 

We say to your father – may Allaah guide him – that Allaah has given you a great responsibility, which is to teach and advise your family, including your wife and children. The Messenger (peace and blessings of Allaah be upon him) said in a hadeeth whose authenticity is agreed upon: “Each of you is a shepherd and responsible for his flock. The man is the shepherd of his family and is responsible for his flock.” 

Allaah has commanded you to protect yourself and your family from His Fire, as He says (interpretation of the meaning): 

“O you who believe! Ward off yourselves and your families against a Fire (Hell) whose fuel is men and stones, over which are (appointed) angels stern (and) severe, who disobey not, (from executing) the Commands they receive from Allaah, but do that which they are commanded”

[al-Tahreem 66:6]

And He says, enjoining the prayer (interpretation of the meaning): 

“And enjoin As‑Salaah (the prayer) on your family, and be patient in offering them [i.e. the Salaah (prayers)]. We ask not of you a provision (i.e. to give Us something: money): We provide for you. And the good end (i.e. Paradise) is for the Muttaqoon (the pious)”

[Ta-Ha 20:132]

Ibn al-Qayyim (may Allaah have mercy on him) said: 

Whoever neglects to teach his son that which will benefit him, and ignores him, has done something very bad indeed. Most children go astray because of their parents who neglect them and fail to teach them the duties and Sunnahs of their religion. They neglect them when they are young so they do not benefit themselves or benefit their parents when they grow up. End quote. 

Tuhfat al-Mawdood, p. 229 

We ask you an important question: Where are you when it is time for Fajr prayer? Is it not obligatory for you to offer the prayer in congregation? Is it not obligatory for you to be a good example for your family and children by praying in congregation in the house of Allaah? If you do that, you will have fulfilled the duty that Allaah has enjoined upon you, and you will have helped your son to pray in the mosque, and you will put your mind at rest if you are worried about him going alone.

Remember that the Prophet (peace and blessings of Allaah be upon him) has told us that whoever prays Fajr in the mosque will be under the protection of Allaah, so how can you fear for one who is under the protection of Allaah, may He be exalted? 

It was narrated that Jundub ibn ‘Abd-Allaah (may Allaah be pleased with him) said: The Messenger of Allaah (peace and blessings of Allaah be upon him) said: “Whoever prays Fajr is under the protection of Allaah, so do not fall short with regard to the rights of Allaah, for anyone who does that, Allaah will seize him and will throw him on his face into the Fire of Hell.”Narrated by Muslim, 657. 

We ask Allaah to help you to fulfil the trust and to make you a good example for your family, and to make you help your son to offer the prayers in the house of Allaah. 

And Allaah knows best.